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?
If I'm understanding your question right, just try and use the same port for the same drives. If you don't by accident you can just adjust the boot priority in BIOS to the right drive.
I believe it will boot anyway it just checks the drives in the same port order you had set it at before to find the OS.
Its been a while since I built a rig or changed out drives but either way I'm sure there will be no big problem, have at it.
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.