Pay by check or credit card

Is it possible to have the pay by credit card synced but be able to bypass it for those who want to pay by check?

I believe you are referring to this setup inside a form. If yes, you can use conditions to hide the payment field if the user wants to pay by check - https://www.jotform.com/help/316-how-to-show-or-hide-fields-base-on-user-s-answer

Let us know if this is what you were referring to. Else, please let us know with reference to your form.

That would work however I'm using Product List and can't find a way to have our Square synced to accept online payments and still allow people to order products to pay by check, the Square is embedded within the product list. Is there a way to separate that out?

Unfortunately, the products and payment fields are considered one field, as such, the show/hide condition won't help indeed.

However, if you only have a couple of products, then you can instead list your products using regular fields then add a Form Calculation widget to calculate the total and pass the value to your payment field.

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

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

This way, the products and the payment field is separated so you are free to show/hide certain fields without affecting the others.

How-to-Show-or-Hide-Fields-Base-on-User-s-Answer