Its a good idea to replace bittorrent with azureus (Vuze).
if you replace it at the moment as your a downloading seeding, then ur torrents will continue to download and seed with bit torrent. Until you designate a file with azureus, it will not open, unless you set it to automatically associate itself with torrent files, which then any torrent file you click on or download will open itself with azureus.
My opinion would be install azureus, keep bit torrent installed until you have completely finished downloading/seeding what you want, then uninstall it and use azureus as the default.
Oh and your downloads/seeds will not transfer themselves into azureus from bit torrent automatically. you will have to go designate a sepcific folder for them etc...
But let us know if you are going to do that, i can giv u steps to transfer ur seeds/downloads to azureus!