Hi David,
As you have probably already noticed, Method currently handles Credit Card data in a slightly different manner than other fields from QuickBooks. Currently, if you store a Credit Card in Method under Customer->Edit Customer->Payment and Info, the credit card information will get synced over to QuickBooks, once it is in QuickBooks, the card number in record appears something like this: XXXXXXXXXXXX5544. Method doesn't actually store any Credit Card information in our database, if a card number is entered into Method, then it will sync to QuickBooks, then be encrypted as described above.
Our development team is currently working on using/adding "Authentication Tokens" to our system. Through adding this functionality, we will be able to pass payment requests on behalf of our Customers directly to the Merchants, without the need to store this info in the Method database. I don't want to get too deep in this explanation of Authentication Tokens, however I wanted to bring it up because once this has been added to Method, our payments process will change slightly, and will likely work better for what you are trying to accomplish.
At this time, Method doesn't recommend or condone storing Customer Credit Card information in our database, we also wouldn't be able to provide any support/help in doing this. With our current setup, you will have to unfortunately continue to manually input this information into the receive payments section each time. We apologize if the way Method currently handles Credit Cards is causing you some issues with your businesses processes. Hopefully ,once we do get the Authorization Tokens functioning in our system, this will allow you to accomplish what you are looking for.
-Ben