The better player should start, almost always imo. In fact, unlike the NBA, Buzzerbeater doesn't seem to give that much importance to bench production. No point in letting your better player sit out for 24-30 more minutes than a starter would just so he can balance the second line.
On a side note, this game doesn't really work in "units" either. Normally, you'll have at least 1-2 starters in at all times as well. IMO, ideally everybody on your starting lineup has 7+ stamina, and the bench players have much better passing and handling skills compared to what an ideal player would have. That way, when the benchies are in, at least they can get the ball to a starter for a good shot.