It depends what you mean by “work correctly”. When you manually mark the invoice as paid (at the point you wrote the cheque) that will create a money out transaction on the bank account. When the cheque is cashed you’ll get a transaction on your bank feed for the same amount which you can safely delete instead of tagging it.
The bank balance will be out of sync between the time you wrote the cheque and the time it was cashed, but from a management point of view you probably want it that way round so you’re working on the basis of the cheque money not being available to spend on anything else in the meantime.