It's up to you when you mark them as paid. It depends whether you're using the Desktop or the Online version as to how you do it, but both systems allow you to mark them as paid before matching it with the bank statement.

If you've entered a bill that's now showing as unpaid, then when making the payment, you can tell QuickBooks as to how it's paid - i.e. via the bank, or via the credit card account, so that the payment logs into the correct place ready for when the bank reconciliation of that account is carried out.

Using the Suppliers/Enter Bill system enters the transaction for payment at a later date, such as on-account bills. If you wish to enter the transactions as a one-step entry, such as insurance direct debits and cash or credit card payments that are made on the same day as the bill/receipt, you can use the 'Expense' (QBO) or Write Cheques (Desktop) method. You select the account you're paying from (credit card or bank) and enter the transaction accordingly, this then puts the payment direct into the system.

With QBO (QuickBooks Online) you have the additional option of marking items as paid direct from the bank feed by either adding or matching the transaction. The one tip I would give if you're using this method, is that when you receive the paper statement and begin the bank or credit card reconciliation, make sure you deselect all the 'auto-ticks' that the bank feed has added in before you begin - otherwise it can play havoc with your balances.

Hope this helps to explain that there is no right and wrong way of doing it - there are just different ways of which you'll find the way that suits you best.

Carol