Here is the process for recording prepaid inventory in QuickBooks Online:
Enter a Purchase Order as you normally would for inventory items.
Record the pre-payment as a Check or Expense using Accounts Payable for the expense account.
The pre-payment will now show as a credit for the open balance of the vendor.
The remaining balance will now show as the open balance for the vendor.
Make a payment (bill payment).
The bill and the prior pre-payment(s) are checked automatically and the difference, if any, is recorded as a check (or credit card payment).