Can I add a separate line item for 3% fee and then add that to the amount the user enters to come up with a total amount to charge?

Can I add a separate line item for 3% fee and then add that to the amount the user enters to come up with a total amount to charge?

I'm not sure what your end goal is so I'll just assume what you meant to say was to add a 3% charge on top of the total amount. But IF AND ONLY IF they selected "Credit/Debit Card or PayPal (A 3% processing fee will be charged for credit/debit card or PayPal payments). Credit card payments can be made in the section below." as their Form of Payment.

e.g. If this checkbox was ticked...

...Then a $100 charge should become $103.

If that's the case, you first need to take into consideration that Checkboxes allow users to select 1 or more options. IMO, you should be using a Radio Button instead (that way, users will be limited to select JUST ONE Form of Payment).

Related guide: Smart-Forms-Using-Conditional-Logic 

Also, how are you computing the Square Payment field charge btw? I don't see any calculations on your form. If you need help figuring out how to perform calculations with a Payment Field, I strongly urge you to refer to these guides:

How-to-Perform-Form-Calculation-Using-a-Widget

How-to-Pass-a-Calculation-to-a-Payment-Field