First off, did you use two separate recorders or a recorder with a single clock.
Second, to some degree you will always get phase cancelation when mixing sources, the degree of such is dictated by how much common information is in both (the more common the information, the worse the cancelation). An onstage recording and a sbd feed don't have as much in common as two mic sources where the two sets of mics are in the same general area. Regarding the later, unless there is something specifically bad about both, I'd pick a single set and just play with that one, but ymmv.
So assuming that you still want to do this, and stuff is clocked correctly, and as kcmule points out, make sure the polarity or phase is correct amongst the channels, then you can line them up as best as possible (I recommend synching on a snare hit to start with personally), and start delaying one source over the other by 2 or 3 samples and listen. I've found a VST plugin works best as you can let it play and change the delay and listen to it. If you're plugin works in terms of milliseconds, then adjust by 1ms at the most and listen. I've found thats enough to hear shifts in balance and cancelation when mixing. good luck.