Hi JorgetteG: 

thank you so much for the notes, I'm using QB desktop, and I enter credit card fees (like Paypal fees) as negative amount in the deposit transactions, below is a screen shot of what I'm working on, I have setup a vendor name "credit Card Fees" in the vendor profile, but the fees I entered in the deposit do not appear in the vendor file. They can only be find in the expenses report.  

I tried to create an invoice under the vendor file and paid it using Vendor / 2100 A/P, the the payment still does not show up in the vendor file, only balance appear as 0.