Sounds about right, what you've got there. Though backing up your system is kind of an optional step here. It's very unlikely something will happen, but then it's always good to have a recent backup of anything you wouldn't want to lose, so if you have a recent backup you can skip that step.

As for how you know which drive is which... Well, generally since you're the one who put them in there you just kind of remember, but it won't really hurt anything to just start unplugging drives until you find the right one.

What I'm not getting here, is why you're pulling the second drive. I'm not seeing anything that explains what you hope to accomplish by this. It looks to me like you're just trying to copy a bunch of files to one of your external drives, and so I can't figure out the need to put this drive inside the computer. You can have multiple external drives connected at the same time without any problem. I used to have 2-3 connected to my system all the time. It might get a bit slow copying files from one (USB) external to another, but you can certainly do it.

Maybe if you give a little detail about what you're trying to do, we could determine whether or not you really need to pull the drive at all.