Golf League Tracker offers two methods to set a Handicap Percentage for your players.
It's important to understand what a "Course Handicap" is compared to the Player's Handicap Index, and that is explained in this FAQ:
Handicap Index vs Course Handicap
It depends what you're trying to accomplish, and what format your league is. If your goal is to apply a percentage to reward lower handicapped player, then you should set Handicap Percent (setting #38). This would be equivalent to the USGA old method of applying 96% to the handicap calculation (fyi, this was abolished with the World Handicap System, which has gone to a full 100%).
However, if your goal is to follow the USGA guidelines for applying a Handicap Allowance because of the type of format your play, you should set Handicap Allowance Percentage (setting #212). If you're unsure what percentage to use, you can take a page out of the USGA handicapping manual and follow their guidelines here.
Typically not, but nothing is stopping you. Just be sure you're not accidentally setting both settings to something less than 1 (100%) when you really want to apply the percentage only once. For example, if you set both to 0.8 (which is 80%), that 80% would be applied twice: Once when the player's handicap index is calculated, and again to the player's Course Handicap.