I assume that your cash register keeps up with sales tax.
[1] Run all Square deposits to Gross Sales - use bank rules to make this easy and automatic.
[2] Set up items for Taxable Sales, Nontaxable Sales, Sales Tax.
[3] Use your daily cash register sales reports to do a sales receipt with the totals and run a negative to an item to "Gross Sales" for the total so that the Sales Receipt has a zero balance.
You will want each Sales Receipt to be coded to the location from which the report was drawn so that you can keep up by location - which often affects sales tax rates. You will also have to recognize that a Square fee is pulled from each transaction and expense it from your Square reports.
