If the tenant has to pay rent in advanced but all the money has to go to the landlord please follow the steps below.
First click on take a payment:

Enter in the amount of money that is being received:

Then untick the checkbox highlighted below. This will make sure that the money will go to the landlord meaning the agent won't hold onto any of it:

Below you will see all the rents that will be payed off with that lump sum of money.