Matt, thanks for the more detailed info, it always helps. I took the time to download the owner's manual for the SPL-1200II. This really helps to see the exact back panel layout on your sub. Also, different brands sometimes use various words to describe the same function. For example, Velodyne uses "subwoofer direct" instead of "bypass" on their crossover toggle switch.
I can't see any glowing problems from what you said but I will simply list the proper settings for your set-up and then some general comments.
...The toggle switch should be set to the "subwoofer direct" setting.
...You should use one of the two input jacks (which happen to be labeled "LFE" ... I think this also confuses many people because it is actually a combination of both low bass and LFE signals presuming you have correctly set the receiver to send both low bass and the LFE signals to the sub), left or right, it makes no difference. You already have a Y-splitter to use both the left and right input and that is fine, just not necessary and costs extra money. Yes, it does increase the output by about 6dB's but the volume dial does the same thing. So it is just a initial volume gain tradeoff.
...An important paragraph on page 7 of your manual states:
This control allows you to balance the output from the subwoofer to the main speakers/amplifier in your system. This control should be set to achieve similar output level from both the main speakers and the subwoofer when listening to music. A good starting point for the volume control is 3 or 4 dots from minimum." (this is about 11-12 o'clock on this sub)
My thoughts: (This is actually a trim control to balance the output of the sub and speakers. So if you had speakers that were very efficient then this control might have to be higher and on the other hand lower if you have less efficient speakers. I'm mentioning this to make sure that anyone reading my post uderstands that the day to day changes in the volume of the sub are a function of the sub volume controls on the receiver and not this control which normally would be sent during set-up and then left alone).
...Your manual also states: "A bypass switch is also provided if you wish to use an external crossover." This could confuse many because they don't mention that this actually is the switch that they label as "internal x-over/subwoofer direct" instead of "bypass." Secondly, they use the word "external crossover" when they should explain that this usually means an A/V receiver. Velodyne as well as other brands do their customers no favors by not making their manuals clear. You should have seen the sub manual on my previous Energy sub, what a confusing mess!
...Be sure you understand the phase adjustment switch as described on page 7. The music should have lots of heavy and steady bass. This is not always easy to hear, do the best you can. Be sure you are in main lsitening position when you do this, helps if you have your dog or some person do this switching on the back of the sub for you.
... THIS IS VERY IMPORTANT On page 8 the "Crossover switch" paragraph is also not very clear. Anyone with a current A/V receiver that has flexible crossover points every 10-20 decibels or so, which most except the very cheapest ones now have, need to use the "Bypass" setting or in the case of Velodyne they call it the "Subwoofer Direct" setting. Sometimes instead of there being only one input with a two position toggle switch there will be two seperate inputs, one normal and one bypass which accomplish the same thing.
... This confusion is made a little clearer on page 12 in the second paragraph. They still need to explain clearly that Velodyne means the same thing when they use the terms "bypass" and "subwoofer direct."
...Thus when you have your sub corectly set to bypass/subwoofer direct the low-pass crossover dial is actually disconnected and not funtional. Leave it set to the MAX/120 just to be safe in case the dog accidentally brushes against it.
...Completely disregard the two, L&R, RCA OUTPUTS.
...The Infinity Primus speakers here, just for other's general information, are the same speakers as the JBL's Northridge and Venue series with different clothing. This is my conclusion because they are from the same parent company and have the exact same specs, size drivers, cabinet sizes etc. Should be very nice sound.
...Just a curious note here but you have an ever so slight mismatch because you use the Infinity Beta 360 center channel rather than the exact matching Primus C25 center channel. I can only presume that you did this to get a "better" center channel. You have a center channel with a different tweeter than the tweeter in the other four speakers. If the tweeter sound on pink noise is identical to the sound on the Primus speakers in your room then no problem.
...Your Infinity speakers all have a low bass response down to about 38Hz-58Hz or less at -3dB. You should set the bass crossover setting on your Yammie receiver to 80Hz. The only other settings I would even consider are maybe 70Hz or maybe up to 90Hz. But this is a big maybe. 80Hz should be the best and I'm presuming here that the RX-V1500 has one setting for all 5 speakers together. If it has bass crossover settings that can be set independently for all 5 speakers then I would still use 80Hz but try as an alternative, Primus 150 at 80Hz, Primus 360 and Beta 360 at 70Hz. What's the reason for all of this? It is to let the sub take over all of the low bass from 80Hz and down and also all of the LFE special effects signals (which yes are different). All 5 main speakers handle the 80Hz and up range. BTW, this is the THX recommendation and also that of most pros.
...Set the bass management points in the set-up procedures for the Yammia 1500 so that all speakers are set to "SMALL" yes I said "SMALL" and that does not mean "large" ... regardless what all of your friends, neighbors, pastor and the "expert" down at the electronics store say. No, I did not receive this bit of wisdom in a "divine revelation" but from reading 235,739 different opinions of real "experts" including Mr. THX and also Paul McCartney (yeah, yeah, yeah)...sorry, but I'm making this post so long (what's new) that my British humor is setting in.
...Also, however that Yammie handles it, send ALL the low bass and LFE signals to the subwoofer in conjunction with the 80Hz crossover point that you selected. No fudging and think that you might just sneak some of that great bass over to those huge floorstanding speakers you bought with the real big woofers. You think, gee, why did I buy those big speakers (I'm thinking the same thing). You bought them in case you couldn't fork over the money for the sub. Also remember they do play from 80Hz and up, still lots of medium and high bass. Plus the larger speakers can give you more power handling if you ever need it and you don't need stands and they look awesome. Hide the sub and your friends will really be impressed with the low bass output of those towers!
...Normally, the only reason to raise a sub slightly is if it has a downfiring driver and you have deep pile carpeting. Some people place the speakers on spikes rather than simple feet. Otherwise, place it on the floor and in a corner or near a wall. The exact placement of the sub in your room, even a change of several inches can make a big difference. Also once you have got the best location for the sub, moving slightly from your main listening position can also change the sub response or loudness. You must keep this in mind, choose your main seat and always be there when you evaulate the sub with just your ears or the RS meter. Don't be surprised if you finally get it so it sounds great and then when you go sit in that other chair over there that you hear significantly different sub peformance.
...You say: "The sub is running directly to the wall." I presume you mean the power cord? Yes, that is good. Don't use one of the power inputs on the back of the receiver. You might if you have thunderstorms, want to use a small, one plug type, surge protector, companies like APC, Belkin, etc. make them.
...A Radio Shack meter is a great tool. Be sure and get the analog model for the best results. The analog model gives you accuracy down to a 0.5 decibel level versus whole decibels only on the digital model. This slight difference is very important for proper level setting for the 5.1 channels. Do not trust you ears! The human ear is not nearly as precise as that meter. I once set up a my Klipsch by ear back in the nineties. It sounded very good but not great to me. I thought maybe I needed a better system for the best sound. Then I read a detailed review using the Radio Shack meter. I ran down to my local RS. Wow, I couldn't believe it. The difference was a system wide smoothness in the surround sound that I did not have before. It was immediatley evident to me. My very accurate ears (I thought) could not set the channel levels much closer than 1.5 to 2.0dB's. All humans are the same (except Stewie). Use this meter to set the output levels for all channels during the test portion of the manual set-up or to verfiy the accuracy of the YPAO auto set-up system. Later you can also use it to do your own frequency evaluation of your system. You would use a CD or DVD with test tones from 25Hz or so and up (especially up to about 200Hz) or so to see what big peaks or dips you might have in the response. You have to use a "corection table" because the RS meter loses accuracy as it goes down to the lower frequencies. Just to match the channel outputs levels you don't need this. Find the RS correction tables with a Google search or I can link them.
...The YPAO is fine (and better than some of the systems on the other brands). Understand however that it is not perfect and is a marketing driven feature to make it easier for newbies. These systems can be fooled and frequently make mistakes. I highly recommend you double check all the YPAO results manually or simply start all over and do a complete manual set-up.
In my opinion you have something incorrectly set in your receiver set-up procedutes and are not getting the full low bass redirection from the other 5 speakers and also the LFE effects through to your sub.
Have fun checking for the problem and especially let us all know what you find.