To monitor your players' payments of regular match fees, training fees or yellow or red card fines, enter the expected amounts when setting up a Season.
Each fixture, when you Pick Team and hit the Next: More Details button, the Match and Training Fees will be defaulted to these expected amounts. Any player who doesn't have to pay (for whatever reason) needs you to set their fee to zero. When you hit Done, these fees will be charged to each player's Account.
Similarly, when you report a game and drag a yellow or red card to a player, their Account is charged by the expected amount.
When reporting a game, hit the Next: More Details button and enter how much each player has paid in terms of Match Fees, Training Fees and Fines. It will probably be easier to hit all at the top of each column then mark those that haven't paid. When you hit Done, these payments will be taken from each player's Account.