The most important thing you can do is have a written constitution that's easily available for everyone to read, which spells out your league's rules in clear English. Some things you'll want to include, off the top of my head:
- How transactions are handled in the off-season (e.g. no add/drops)
- Deadlines! By what date the draft must be decided, when keepers must be set (e.g. 1 week before draft)
- How kept player value changes (salary increases, draft picks, etc.)
- A process for changing the constitution- things will come up every year, and you'll want a smooth process for incorporating those rules. You may want to take a "commish has final say" approach, or have a voting system.
- A very clear veto policy, even if it's a "no vetoes" policy.
- If you're using minor leaguers, clear rules around when a player can be kept in your minor-league slots vs. active roster