I always just kept them both to the same, as if I had 2 big bass drums. Ankle weights can help too but what you do on one foot, try to do it on the other, leading with the left foot, or anything like that. (If you lead with the left, it's not quite on beat unless you have a left handed kit.) When you want to cover some bands like meshuggah, Dillinger Escape Plan, ..., it matters where you put each bassdrum note, on the beat, E, &, A, or even between any of those. However this is a lot to digest so if you are going to try it, keep it well below 100 bpm to start, and make sure you use a metronome or ClickTrack.
I have been practicing this for 5 years and I still dont have it to a level im proud of, so dont be discouraged if you dont get it at first.