not a problem to run even same version of utorrent at once, the only thing that would be recommended - is to change skins at one of them to differ them in taskbar
links above aren't too helpful, here's the correct ones
How To Run Multiple Instances of uTorrent (v1.7.7 & v1.8) | THE source for BitTorrent & P2P Tips, Tricks and Info. | FileShareFreak
Download uTorrent 3.0 Beta 25252 - FileHippo.com
i'd recommend last generation stable builds all of its kind - 1.8.5, 2.0.4 or the forementioned 2.2.1, it all depends on features, utp functionality, ipv6 (not sure when it appeared), tracker compatibility, resource hogging etc. also you should know where all your setting / .torrent stuff is located, in case of using an external disc, it would make sense to put all your tech date there so if the disc is unplugged, utorrent just won't start...
another good thing to do is to put all setiings in dropbox controlled folder so you'll have all your data backups in case of a rainy day and if some error will occur, you won't have to rehash stuff, just restore it from early state from anytime of the last month....
the only and most powerful tool to move settings, your torrent data location at once is bencode, you can google for instructions, it's relatively easy, just don't forget to make backup of your settings before you'll start.