You need to enter two transactions.
 
First you need to enter an A/P Voucher to the Vendor. It doesn't matter what GL account you choose (see the next step). Then pick both the credit memo and voucher and print a check (it will be $0.00) to get them off the books.
 
Now your Vendor account and aging are correct but you still don't have the money and you have a rogue entry in your GL.
 
So now you enter a Type CR G/L Journal Trans using the Bank Account that your are depositing it to. Enter two lines - one for your bank account and and one for the account you chose in step 1.
 
There may be more elegant ways, but that's how I do it and it works.