Vendor Prepayment in QB

If this is short term:
1. Issue a PO and then a bill or just a bill and note it as a prepayment.
2. Pay the bill through the pay bills window.
or
If you just want to post a check to match a bill later
1. Click the check icon or go to Banking>write checks
2. Choose Accounts Payable in the account drop down list on the expense tab of the check and the Vendor name in the Customer:job column.
3. When the bill comes in, enter the bill in the Vendor Center
4. Go to pay bills and select the bill.  Down at the bottom right there will be a credit available to post against the bill (this credit was created when you wrote the check)
5. Click the Set Credits Button and complete

If this is a long term Prepayment
1. Enter a bill and use the Prepaid expense account you are using in the Expense Tab drop down list
2. Pay the bill and this will post the prepaid expense for the check you are issuing
3. When you receive the 1st invoice enter a bill and use the appropriate expense account in the drop down list on the expense tab.  This will post the current expense
4. Enter a credit for the Vendor and in the Expense drop down list enter the prepaid account, this will post to the prepaid expense account.
5. Go to Vendor>Pay Bills and choose the bill and select set credits to post the credit to the bill.