We did this together in a 1 hour premier support session. If you have it working with another payment gateway like authorize.net or paypal direct payments, then swapping out the code for square is pretty easy.
First I would set up a test page outside of the site to get a working square transaction to make sure your credentials are all in place. Then I would move that code into your checkout process and swap out the test values with the references to your checkout form and ecart contents.