Yes, of course you can!
Indeed, you can have as many WinUAE folders floating around on your system as you wish, although I recommend giving them different names to avoid confusion...
AIAB's WinUAE configuration is intended to be portable, using relative pathnames; you should effectively be able to move the folder to any location - simply ensure you have a a WinUAE.exe executable in the same folder and a KS3.1 kick.rom in the 'Roms' directory, and start the emulator - it's as simple as that.
For example, I have a customised copy of AIAB on my keyring flash drive which uses this method, and as long as I have access to a USB equipped Windows PC, I can boot into my Amiga within a matter of seconds. Recent changes to WinUAE's registry settings may occasionally cause it to refer back to fixed, absolute paths, however simply clicking the 'Reset registry' button should restore everything.
Whilst integrating the numerous new features in this 'hisashiburi' AIAB update, I had numerous folders littering my desktop, each with different WinUAE betas and configuration files; some with PNG icons, some with GlowIcons, some without any icons at all (!) - if I was limited to one Amiga emulation installation, life would have been very difficult!
Take it easy,