CAUTION: This guidance is from the perspective of a business owner that is willing to risk minor fines and penalties in order to save time. For more information see The Hackers Guide to Payroll Taxes Philosophy.
If you are using Monchilla you shouldn't need this, but if for some reason you underpay or overpay an employee you can use this trick to adjust the net pay to make the paycheck match what was actually paid.
If you overpaid an employee by $100 you can change the paycheck to add an employee advance of $100 and then later have that advance paid back.
If you underpaid an employee by $100 the best solution is probably to simply write a separate check to the employee for the amount that you owe them. When it is time to reconcile a the paycheck you will have two bank transactions that you need to reconcile to the single paycheck (the amount you initially paid the employee and the additional check you wrote), but this is pretty easy to do.
Alternatively you could have them pay back an employee advance on the check that you underpaid. In this case their "advance account" will actually be negative indicating that you owe the employee money. On a future check you will issue an employee advance to pay them back the money you owe them.
You might notice that this is exactly opposite of what normally happens when you first advance an employee money and then later they pay it back. In this case you essentially took a loan from your employee and your paying it back later, but you can still use the employee advance concept (in reverse order) to record this accurately in your books.