I use the Premium version in exactly the way you describe. I have several accounts: some banking, some credit and some debt. Each time I record a transaction, I’m given the option to record both the envelope (e.g. Gas) and the source of payment (e.g. Mastercard). When I make a payment to the card, I do an Account Transfer from my checking account into my Mastercard which keeps the balances in both accounts correct but doesn’t affect how I’ve spent my money on the Envelope side of the budget at all.
When you import transactions, you import them into the appropriate account, so you’d import all your Mastercard transactions from the time period you specify. It will match up the ones you’ve already entered (but allow you to confirm or change them if necessary, which is rare) and let you assign any that were overlooked to the appropriate envelope before adding them into your ledger.
(I added screen shots of a Transaction entry where you can choose an account and an Account Transfer when you make a payment on the card.)
Hope that helps!
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