If you mark an invoice as paid, it asks you how you paid it, e.g. by bank or by cash. It will then be recorded in the books in the bank or cash account. So it is already there, if you add it to a bank statement again, you register it twice. You could probably setup another account as intermediairy (bank-needcheck), so when you click "pay" you don't select bank, but select bank-needcheck. Then when you import your bank statement on each line you enter bank-needcheck as account. Not sure I would call this best practice though.

If you opt not to press pay at the invoice, but use the bank statement, you can create a bank statement and click "import" (which is a rather confusing term, it has nothing to do with importing a file). It will then show you a list of unpaid invoices and you can select the ones you see on your actual bank statement. These invoices will be reconciled and marked as paid.

If you want to do an import of your bank statement, e.g. from excel (csv), you do it in two steps. First you import the file, then you click on "manual reconcile", where you can match your bank statement lines with your unpaid invoices. Here you'll probably run into some trouble, as you have to make sure that in your import each bank statement line also contains the correct partner. Another way of reconciliation is to open the accounts payable/accounts receivable journal and select the two matching lines and then click on "More" button where you will find reconcile. Both ways will set the invoice as paid.