Even you didn't know it, there are manuals or docs that supply the info or point you to that answer. In most cases though during the intial other than what is considered "deafult" as in 1-backup device, it usually falls into place. In the extra storage now provided, then you have either reset/set that both are present and accepting the way you back-up. -OR- you direct after one is done that it continue to the next. All this data swapping is bound to slow down or cause some heavy PC usage, so time this for off peak period of your usage or not when being used, thus idle period or at set time.
YES, it would be best to maintain the same devices(and s/w) in general as you deal with similar issues of setup, yada, yada, etc. Otherwise, you would have to sort this out on different brands or back-up s/w. Understand, the limits or parameters of how this is all supported, once you leave the typical setup, things usually get complicated.
One lesson, I found that works pretty decent is the use of "HD docks". Here you can simply swap HDs as needed and thus using 1-HD the s/w sees a need to update(or back-up) and takes off. While this is a direct physical exchange of HDs, the principle is the same just the added step of switching the HDs now and then. The s/w itself is nothing special and is at default levels as I recall.
tada -----Willy
I have a PC with a 1 TB hard drive, backed up locally by a WD My Passport drive. I would like to get a second drive as a second backup to keep offsite & back up on a regular basis. Would it make more sense to get the same type of device (WD) or a different one? Will getting the same device confuse the WD software? Grateful for your advice.

Chowhound
Comic Vine
GameFAQs
GameSpot
Giant Bomb
TechRepublic