Rentables is a trust accounting system, meaning that it keeps track of who the funds in a trust account (or escrow account) belong to. When you select the Payee for a charge you are designating the beneficiary of the charge. This is independent of the fact that the check is made out to the property manager.
A Closer Look at the New Payment Form
The payment form has two parts. The first part (Step 1) is recording money received. This is usually a check made out to the property manager and deposited in their trust account.
In Step 2 on the form, you are applying those funds to a charge (such as Rent). Notice that here you see the owner as the Payee (which is derived from the payee you selected when recording the charge). This is the point at which funds are being reallocated from the tenant's ledger to the owner's ledger.