If you want to write a check to a credit card company, there should be no need for a manual entry as BQE CORE handles it automatically just like any accounting software does. In CORE, you can go to Accounting > Checks and apply a payment from your checking account to your credit card account. Doing this updates both the checking and credit card accounts automatically. This entry credits your bank account and debits the credit card account, thus reducing your liability. Check CORE Help Center for details.
If you just need to debit one account and credit the other, then you can use Fund Transfers. Check CORE Help Center for details.