how do i apply a prepayment of 2000.00 to a supplier account

You can record the advance payment as an expense affecting Accounts Payable (A/P). This allows you to apply it to your future bill. Here's how:
 

1. Go to + Create, then Expense.
2. Select the payee and payment account.
3. Under the Category column, choose Account: Accounts Payable.
4. Enter the description and the amount.
5. Click Save and close.

If you have any questions, just drop a message in the thread.