Square: Registration & phone reader

Do I have to set up an account for jot form for my website and another for Square for my phone reader?

1) First you need to signup with JotForm. Its very fast and easy to do this:

https://www.jotform.com/signup

2) Then you will need to register with Square (if you haven't already done so)

https://squareup.com/signup/us?lang_code=en

Now as far as I'm aware you wont be able to use your card reader to pay with JotForm. But in fairness your customers probably wont have a card reader anyway. They will be able to enter their credit/debit card details to pay instead.