As best I can tell:

1. Division winners are 1 seeds
2. Divisional runner ups are 2 seeds
3. Wild cards are 3 seeds
4. Head to head is the first tiebreaker
5. PPG is the second tiebreaker
6. Goal difference is the third tiebreaker (averaged by # of games if different numbers of games were played)
7. Goals scored is the fourth tiebreaker (averaged by # of games if different numbers of games were played)
8. More stuff
9. Sometimes they decide to do different things depending on travel distances or whatever. #USL2

Sources: 1 2