Krausero,
You can record this pre-payment and have the vendor show a credit balance until the actual invoice is received. If you are using PO's you can reference a PO# on the pre-payment to help identify a specific pre-payment when you apply it to an voucher later.
I think in your specific case, since the $ has already been debited, there is no need to print a paper check. You can create a pre-payment document using Quick Voucher/ Prepayment, then use Manual Check Entry to create the Hand Check or Electronic Payment record. Reference the pre-payment in the grid's reference number in Manual Check Entry. (This is how we handle wire payments at my site)
Then you can apply that pre-payment to a voucher once it is created. You can apply it directly in Voucher and Adjustment Entry (this step releases the voucher, and applies the pre-payment in one step) or in Pre-Payment application.
This is a link to a post I created about this topic last month.