With Golf League Tracker, you can award points based on the position a player finished against the field, with their gross score (no handicap) or net score (with handicap). You can even combine the two if so desired. For the following examples, we're going to be using the Net score, but the concept and configuration is the same if you decide to use the Gross score.
Consider a league of 8 players, and "payout" for the top 4 places of 10, 8, 6, and 4 points with the following scores as displayed in the "Individual Stroke Play Results" report in the statistics section:

To set Golf League Tracker up to handle this automatically is very easy:
A percentage based payout is where the number of points distributed for the round is based upon the number of players who played for that week. Often this format is used for a pool of money. In this example, let's say each player put in 5 dollars, and you pay out for the top 3 places of 50%, 35%, and 15%. In this case, you need to set two settings in your league configuration:
With this setup, recall we have 8 players, each worth 5 points, therefore the total "pot" is 40 points. First place pay 50%, so the first place player won 20 points, 2nd place pays 35%, which is 14 points, and 3rd place pays 15%, which is 6 points.

Split Points
With split points, any positions which are tied are averaged together. Going back to the first example of 10, 8, 6, 4 points, if 1st and 2nd tie, the 10 and 8 are averaged for 9 points for those top two players, and the 3rd place player wins 3rd place points:

Full Points
With full points, both players who tied won the full amount for that position. In this case, 1st place wins 10 points each. The next player in the standings wins 2nd place points, player after that 3rd place points, and so on. Using full points can result in awarding more positions than expected because of the ties. In this example, 5 players won points instead of 4.

Ranking Points
And finally with Ranking Points, the full point amounts are won by the tied players, but the tied places are skipped over. In this example, Jake and Bernie each won 10 full points, but 3rd player wins the 3rd place points rather than the 2nd place points (as when using "Full Points")

I don't think there's a right or wrong way to set up your points. If you want a linear distribution, just start with 1st place being equal to the number of players or teams you have and go down 1 point for each. If you want a larger bonus for finishing higher, than weight the points for the top places more heavily than the bottom places. You could copy the FedEx cup points listed here if you want a starting point. I recommend using 10% of what the FedEx cup does as it's easier to manage and just looks better in the standings.
Besides awarding points for individual players, you can set this up to award for the team total score or team best ball score, in the case of 2-player team leagues.