As long as you have at least 2 opposing holes on each pipe, you are good (top bottom, side side) The next pipe doesn't care which two it's neighbor is using.
You could of course use 3 or 4 where they fit and are not stripped, but no matter what, tighten them evenly across the entire flange, and in steps like any other sealing surface, with lube on the threads. I like silver antiseize best, it seems to stay put for decades