Before you begin your league for the season, there are some things I recommend reviewing and checking off your list to be sure you're ready for your season. Golf League Tracker can handle dozens of different scenarios, but you need to determine your own league rules for your specific league.
Write everything down. Golf League Tracker has a "League Rules" section in which you can enter your league rules so everybody knows what they are. The last thing you want is controversy in your league because you didn't think of a scenario which now has come up, and requires a decision by you, on the spot (even worse if you or your team is involed in the outcome!). Here are some things to consider:
How are you going to handle absent players and forfeits? If you're playing for points, are you going to let absent players accure points, or do they receive 0? Some, like in my own league, limit an absent player to a certain amount of points (I set the max to about 1/3 of the possible points). If you play 2-player teams, you have the option of having the solo player play for the absent player, or have the course play for the absent player.
Are you going to cancel the rounds or make them up, and when are you going to make them up? Often this decision is in cooperation with the golf course. Courses which are more organized and structured have a plan laid out already. In my league, we keep it simple: We move the rainout to the next week and push the whole season out a week. This keeps everything in the same order (but may change which side you're playing; again, check with the course).
What about rules for rainouts? Who deems whether you're playing or not? Is there a minimum number of holes required to play before the round counts?
How much are you playing for and what's the payout? Come up with a payment structure before the season begins. For example, 1st might get 30% of the pot, 2nd 20%, etc. Keep books on the payouts and make it transparent so everybody can see the money in and out.
Can subs play and how is that handled? In my league we charge subs to play and put that money towards the prize fund.
Tie breakers for season standings are up to you, not Golf League Tracker. Golf League Tracker reports a tie as a tie, so you need to come up with your own plan on how you want ties to be handled. This is league specific since each league can play to different formats, so there's not a solid one-size-fits-all system. In my league, I go back to the previous week and whichever player/team was leading breaks the tie. This gives you the ability to go back as far as you need, and works when more than 2 players or teams are tied.
Make sure your schedule is created for all the "normal" rounds that you plan on playing, and that all players/teams are scheduled that should be. If you've been setting up your league before your season and changed the number of players last minute, you need to make sure you re-generate your schedule so that all those players are accounted for. Check to make sure you selected the correct course and side that you're playing for each week.
If you play position rounds, be sure to mark those as position rounds BEFORE you auto generate the schedule. This will insure the system skips over those rounds when creating the regular season schedule.
If you break your league into multiple segments, be sure to set those segment breaks so that your points reset when you want. This can be adjusted after the fact easily, but it's one more thing you won't have to worry about mid-season.
Have you reviewed your handicap system and settings? If you're a returning customer, you most likely don't need to do anything here, but if you're a new customer it's something to consider. Golf League Tracker has default settings for handicapping, but also has 15 or so settings to customize the calculation the way you want. If you're coming from another system, you may want to try to match however you were previously calculating it.
If you have players playing different tees, be sure you enter those tee boxes and assign them to their proper tees before the season begins. If you have rules as to the qualifications to play certain tees (i.e. by age, by handicap, etc), write those down in your rules section. You also will need to modify your handicap settings to account for the difficulty of different tees.
As a league manager, things are much easier to correct when you enter scores in a timely manner. You should enter scores before the next round is played so handicaps are updated accordingly. Set up a system for yourself so you enter the scores at the same time every week. Don't accumulate 2 or 3 weeks of scores.
For myself, I enter scores first thing the next morning after our round. This allows players to review the scores in case I made a mistake or someone else made a mistake writing down scores. I don't pay out any contest winnings (e.g. skins or closest to the pin), until the following week. I've had instances where a player wrote down the wrong score for someone which affected payouts, so this is so much easier to correct before the money leaves your handicaps.