You can limit how many strokes will be counted on a hole when calculating handicaps in the "Hole Stroke Limit" section of your league settings. These limits only affect the handicap calculation and not points or total score.
You have the option of setting different maximums for different handicap ranges, although most leagues set the same amount of Net Double Bogey for all players.
To set the limits in Golf League Tracker, you will go into your League Settings in the League Setup tab, choose Hole Stroke Limit from the settings category list, and edit one of the values. You can have up to 6 different ranges of handicaps if you want to apply different limits to each range.
For more help see the Golf League Tracker YouTube Help Video on setting up Hole Stroke Limits.