You just need to do a Payment Owner. Go to transactions and click on the down arrow ( left hand side) Choose Payment Owner.
Select the Owner/Property that you paid out, the amount should match the amount you have paid out, if not just type in the amount you manually paid the owner.
Check the date make sure it is the same date that you actually did the transaction. Click OK, process as normal
This transaction will now take the money off the owners balance and put it in the reconciliation screen as an unpresented item.