I was wondering, I have Quake 3 Arena installed in 98, I want to install Q3a in 2000 in the same directory as my q3a folder in win98? Or does it overwrite it? This is a dual boot btw.

You do'nt need to reinstall it.
Unlike many windows apps it doesnt put any files into the windows directory ot any vital information into the registry. it keeps everything it needs in it own directory so the most you will need is a shortcut on your desktop or taskbar.