1. I use my credit cards to pay suppliers.
  2. I then reimburse myself direct from the company bank account.
  3. How do apply the payment to the credit cards, & therefore zero them out ?

There are 2 ways to go about this depending upon the volume of transactions involved:
 
1. Low Volume of transactions.
 
  • Use a bank clearing account or setup one for the purpose called Bill Payment Clearing. Pay the supplier invoices using this bank account and then when you repay to your credit card allocate the payment to this same account. The end result is that the clearing account will have a $0 balance.
 
2. High Volume of transactions
 
  • Setup the credit cards as actual credit card type accounts in shoebooks. i.e. One of Amex, one for Visa etc.
  • Then pay the supplier invoices using these credit card accounts as the payment account.
  • When you repay transfer the funds to the relevant credit card account.
  • Then you can go to credit cards under the banking menu and view these accounts like any other bank/cc account. You will see the supplier payments and the repayments in the register. The difference will be the amount owing. You could even put all the credit card transactions in the system and allocate any private to your loan account. Then you could reconcile these credit card accounts.