Not sure what to do with entering vat on qb from eBay sales if vat and fees have already come off when deposited into my bank daily?

Hello First4cables-gma, 

So if you have vat on the invoice receive the full amount on the invoice to undeposited funds> then create a bank deposit, selecting the invoice> adding the fee account to the account column of the 'add funds to this deposit' section, if there is vat on the fees then you will also have to add that on, enter amount as a minus, this will then show the net amount which you can then match to the amount that is received into your bank account.