So, tomorrow I'm going to be doing some long overdue wire management for a PC I just built. One thing I never really thought about was, when you unplug your SSDs does it matter they get plugged back into or does the PC go off of the MBR?
Upto this day I haven't figured out how Disk Drive Names work. I'm not sure if port C:// D:// etc are software based or that they're called that way from the Motherboard. But like @Kaamos_Llama says, it should boot anyway. I think the BIOS / Motherboard will search for a drive it can boot from prior to doing that so it will always boot into Windows.
@Inspireless Llama Drive letters are assigned by Windows. Not related to what port they are on. You can change them if you like when you install a new drive, but if you try to do it on a drive with applications installed I believe it screws them up.