There is a known problem with using QuickBooks where payments are deposited to your bank account in a deposit that has the fees already removed. This occurs if your credit card processor does "net deposit" (as opposed to gross deposit) or if you're getting payouts from HomeAway or Airbnb. This is a known problem and something we are working to fix by adding in fee and deposit records to OwnerRez so that the differences push across.
In the meantime, for any of these "net deposit" payments, you have to figure those out by hand and then create a "Bank Deposit" record in QB with the fee difference subtracted.
So for instance, if you have 3 payments in OwnerRez like so:
$ 500.00 - Payment 1
$ 250.00 - Payment 2
$ 75.00 - Payment 3
$ 875.00 - Total
But the actual deposit to your bank account is $800 because the processor (or channel) removed $75 in fees. So your payment records in QuickBooks, pushed over by OwnerRez, equal to $875 but your actual deposit is $800. Now what?
Manually create a "Bank Deposit" in QB, select the 3 payments above, then make an inline adjustment on the deposit for $-75 (negative 75) and categorize it against expense account "Bank Service Charges". That will make the deposit sum up to $800 even and match what was deposited. You can then select the bank transaction that was imported (if you have that turned on) and match it up.
Please Note: For this to work, you'll want to make sure your QB settings are set to deposit to the "Undeposited Funds" bank account and not your actual bank account. This will make sure that payments are not auto-deposited to an account but are shown as available to be selected when creating the manual deposit outlined above.