I also use Quickbooks and Square Loans.
To begin with, I have marked "exclude" on the loan deposit in Quickbooks, so the program doesn't count it as income. (Depending on the version of Quickbooks you have, it may allow a more elegant way of designating the loan money so as not to count as taxable income.)
I then create an expense transaction in Quickbooks, under cash accounting, for the amount of the loan fee. I name it "Square Loan Fee", and upload a copy of the loan agreement as the "receipt" to prove the expense.
After that, I just use the amounts deposited to my bank - exactly as Quickbooks sees them - to calculate my business revenue/proft. Although this doesn't track the amount spent on fees, that amount would be tax deductable and subtracted from your revenue anyway. I personally don't think it's worth creating separate accounts to "do it right", since the numbers work out the same and records exist for regulatory agencies to peruse if they were to raise questions.
The only thing special I do is related to sales tax (assuming you have to collect them in your location). Using the amount deposited in the account to calculate sales taxes owed would shortchange the government (since the deposits are less than the actual sales). So instead, I just download a CSV file showing a summary of transactions, which easily provides the sales tax total.
