Usually, if you have public torrents running (and by public I mean non-BakaBT), most of your traffic will go to them, because that's where all the leechers are. Out of around 600 torrents I have going, about 50 are public, and my upload traffic is probably around 50% BakaBT and 50% public.
Stick with just BakaBT torrents for a while and monitor how they're doing. You should probably reset your client's stats by removing and re-adding the torrents.