Back up on second hard drive

I have a second internal hard drive on my pc. I want to change the motherboard, so I want to back up my files to the second hard drive (drive D). My question is, once I install a new motherboard and reinstall Vista Ultimate, will that second drive be recognized, and, if so, would I have to treat the backup as being done from another computer??

Sorry. I thought changing motherboard involved reinstalling vista. It didn't as I found out.