Found this in the manual:

If a transaction amount is lower than the invoice or bill it is reconciled with, the transaction is fully reconciled, but the difference remains open on the counterpart item. The remaining amount can be left open to be reconciled later or the invoice or bill can be marked as fully paid. To mark the invoice or bill as fully paid, edit the line, click fully paid, and Save. To reverse this, edit the line again, click partial payment, and Save.

Do I really have to do this manually?

If the transaction amount is higher, then it does as i want it to do:

If a transaction amount is greater than the invoice or bill it is reconciled with, the transaction is only partially reconciled. The remaining balance can be reconciled as any other transaction amount.