Looking for best way to have a user choose to pay online (paypal) or submit and mail in check?

I think you may have both on your form, but you will need to perform the calculations in order to have the final amount and then pass such amount to the payment field in case your users select PayPal.

These guides will help you doing so: 

https://www.jotform.com/help/259-How-to-Perform-Form-Calculation-Using-a-Widget

https://www.jotform.com/help/275-How-to-Pass-a-Calculation-to-a-Payment-Field 

This guide will also help you either showing the payment field in case your users want to pay using PayPal, or hide it if they want to mail a check, if the select check as payment method you may provide them with the instructions to send you the payment: https://www.jotform.com/help/316-How-to-Show-or-Hide-Fields-Base-on-User-s-Answer 

If you have any question, please let us know.