From my understanding there is categories and their services. You have to make sure that it is not the category but the service that you are putting into the integration drop-down in the invoice section. 

Hi Allie!

Using the QB and HB integration, you should see 3 things coming through to your QB:

1. The invoice for the total (gross amount before fees) 
2. A payment for the total (gross amount before fees) linked to it’s corresponding invoice 
3. A deposit bank deposit -- this one should have the total, the fee, and the net (the same amount that hit the bank)

When these all show, you should be able to see a match in your bank feed and match it. (https://help.honeybook.com/en/articles/2209061-how-to-match-honeybook-invoice-payments-in-quickbooks) 

Could you take one of your client payments and see if you’re able to see these 3 things for them? I’ve attached screenshots of what mines look like so you have an idea what you’re looking for. 

Something else I could think of, would be if maybe you have an HB Capital Loan that maybe those capital loan payments are not showing up broken down on the deposit, we can look into it further, because they should be showing up on there, but again that would only happen IF you have a Capital Loan, if that’s the case,

Let me know how else I can assist you!