Square fee keeps adding extra deposit to my Chart, and if I remove it it makes the invoice unpaid

the way it should work is in QB use receive payments, for that invoice add on the next line the merchant fee expense account and the amount as a negative number, then download and match

That did seem to work. Thanks!

But doesnt that skew my reporting? I took $100 from her but her invoice only says 99.90 now. Or am I thinking about this wrong

Let me provide a few information about how this affects your reporting, Ptonjalken.

As mentioned by Rustler, you'll have to use the Receive Payment option in QuickBooks Online (QBO). Then, you can go and match the transactions entered in QBO to your downloaded transactions. I also recommend reaching out to your accountant for other ways on how to record the fee. 

For more information, you can check this article on how to reconcile an account in QuickBooks Online. 

You'll want to browse these help articles for your reference.

Keep me posted if you need anything else about recording bank fees. I'll be right here to help.

Thanks.

So I can definitely balance the books the way mentioned by putting the negative amount on the invoice.

But I feel like I am logging the fee incorrectly this way? It feels like I am lieing to quickbooks to make it balance (by saying the customer gave me a smaller amount to accommodate a smaller invoice, when in reality it is the fee that is being excluded). 

Is there no way to keep the invoice proper, log the proper amount charged and accepted, and include the square fee as an actual expense? This method feels like I am skirting around a different issue.