Basic Question...I think?
I have a dual boot system(XP Pro and Vista Ultimate). I just made a third partition for files. Is it ok to Move all my "Program" files to that partition or will it mess things up?
You'll need to change your program files system variable but otherwise moving them shouldn't cause problems.
To check go to a command prompt and type echo %programfiles% and check it points to the new location.
If you want to share program files between XP and vista that won't work in many cases and being a different OS many programs are different between their XP and vista versions.