Quickbooks Deposits Not Matching Invoices

I saw an all-call go out for your help on your question. I am still learning Quickbooks myself, and will do my best to answer your question.

When you make the customer card, you can sync it over to Quickbooks so you don't have to do double entry. Search the client on Quickbooks, then on the top right of their card, there's a green button "New Transaction". Click receive payment, and enter the deposit amount you've collected. That will create something to match to the bank statement.

Of course when you collect deposits with Jobber payments, Jobber takes their cut. On the bank transactions page, click on the deposited money, match it to the received payment you've created, fill in the full amount , then at the bottom you'll need to resolve the difference. The difference is Jobber's fee. I have an account set up in my chart of accounts to track Jobber's fees. 

Then the deposit is matched to their account and can be later applied against the generated invoice once you move it to Quickbooks.

There may be a better way to do this, so I'll let others chime in on that.