Customer Under quickbook has a negative balance when there shouldn't be one I received all payment and it says there's and open balance of -319
Editing the Invoice is the wrong way to approach having a fee for received payment deducted. You MUST record full payment against invoice. You can edit your Deposit to deduct the fee as a negative expense on the deposit which makes it correct.
Alternately you could create a Customer Credit Memo for the fee, and apply the memo to reduce the invoice balance to equal what was actually deposited.