I don't really think any changes you make to the funnel settings products (aka 3rd party membership access area) will affect the way your products work (for stripe or other credit card processors).
The only things you should keep in mind are:
1st the products under the PRODUCTS tab are the only ones visible to your customers to purchase, While the ones at the backend settings are only used for tracking with 3rd party gateways such as Paypal.
2nd The same way you've connected your PRODUCTS tab products to your autoresponder (Market Hero) you'll have to do the same thing for other products within the backend settings (3rd party membership access section).
Other than that, there is nothing you need to do.