@agubax 

When you create the deposit, create three line items:

$2,400 to A/R for the customer (not Love's)

-$48.00 to Factoring Fee expense

-$1,255.67 to the Love's fuel card

That will leave $1,096.33 for the deposit amount.  You will then need to match the $2,400 A/R credit created by the deposit to the invoice sold to Love's.  Go to New > Receive Payment and apply the credit to the invoice to close it out.  Keep in mind it will appear as though the payment came from the customer, not Love's, so you may want to create a tag or memo that denotes that. 

The other option is to add the negative expense and fuel deduction to the invoice and then use Receive Payment to match the amount received ($1,096.33) to the amount now due on the invoice.