The reference guide is still work in progress.
Also ability to enter uncleared bank transactions is relatively new feature and not quite finished yet from usability point of view.
If you are reconciling and can’t reconcile a day because the cheque is missing, click
Spend money button during reconciliation and enter the missing bank statement transaction. The key is when entering bank statement transaction is to categorize the payment to
Uncleared payments account, then select the cheque which has been presented.
This will allow you to reconcile the bank account and at the same time it will clear the cheque.
In future, bank reconciliation screen will offer you to simply mark the cheque as presented on that day without manually creating bank statement transaction (Manager will create that bank statement transaction automatically)