Hello, Stefanie.
There isn't an option to apply prepayment for your supplier's PO since this is a non-posting transaction. That said, it won't affect your books.
However, if you need to record a prepayment for your vendor, we can create a Check or Expense and associate it to the Account Payable. This will record as vendor credit and can applied to their future bill.
If you need guide on how to make a check or an expense, see this page for you guide:
Let me know if you have other concern.