This is how to reconcile an incoming payment from a letting agency that includes one month rental payment, tenant deposit, and also deducts the letting fee.

• Make sure the rent invoice is created on the tenant page (this should be done automatically based on the lease dates) e.g. £1000
• Pay the rent invoice from the lease page. Make sure to insert same date and account that the payment was paid out to you by the letting agency. 
• Pay the deposit invoice from the lease page. Make sure to insert same date and account that the payment was paid out to you by the letting agency. 
• Create a property expense for the landlord e.g. £500. The supplier should be the letting agency.
• Pay the letting fee invoice. Make sure to insert same date and account that the payment was paid out to you by the letting agency.
• Under Banking you will see a payment of £1500
• Next to the payment, click the search dropdown and select Batch Payment.
• Under the Existing Payment dropdown select the following 3 transactions: -£500 payment you've created for the letting agency, £1000 rent payment, £1000 deposit payment. (Make sure to select the outgoing payments first, then the incoming payments).
• The total payment amount will now match the bank amount of £1500.
• Click Save.