Card, cheque and other invoice payments go to Undeposited funds. A deposit now moves several of them to a bank account as one entry, so it matches the single amount on the bank statement.
Under an imported transaction of money in, choose Record as a deposit and tick the payments it is made of. Payments that come to the transaction's amount are ticked already. Fees a card company kept are added to Payment processing fees. Undo on the transaction reverses the deposit.
A bank account also has Record deposit for deposits without an imported statement, and the Accounting overview lists how many payments are waiting to be deposited.