Is it possible to let users decide which payment method they want to use?

I have credit card payment on a form but sometimes customers need to send me a check. Is there a way to have my Stripe integration in the form and a way to override it if a client ticks a box to pay by check?

It's possible to do that, but you will need to change the current payment settings, instead of having the products configured on the payment gateway directly you will need to manually perform the calculations, this way you can pass the amount to the payment field is they will use a credit card or simply keep the amount for the check instructions. 

The following guides will provide you with the needed ideas about how to perform calculations and pass the amount to the payment field: 

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

https://www.jotform.com/help/301-How-to-Assign-Calculation-Value

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

This guide will help you showing/hiding the payment field or check instructions based on the user's selection: https://www.jotform.com/help/316-How-to-Show-or-Hide-Fields-Base-on-User-s-Answer 

I hope this helps.