If there is an easier way, I'd like to know... but here's how we do it.
 
Use AP-B a create a voucher for the amount of the credit offset with say a misc GL account (office supplies, etc.).
 
Use AP-B a credit a Credit Memo for the amount of the credit to be applied and use the same GL account as used above.
 
Then via AR-C apply the Voucher against the credit AND apply the Credit Memo against the balance due in each account respectively.
 
Note:  use the same date on all transactions... it will make your life easier in the long run.

Per Lynn, with the latest update if you go into the one account with the open credit and choose the credit and post it, it will then ask you if you want to apply to another customer.  This also works if you get one check that must be applied to different accounts.
 
After clicking yes for posting it takes you back to the payment screen with the credit amount already filled in and you choose the account you would like to apply it to.
 
We have tried this and it works!!