New Wholesale Vendor - Need info on app design

Shopify Partner
6 0 4

We've got a wholesale business selling printed promotional products and have been researching building an app to sell in the App Store for Shopify. Can anyone tell me how the billing piece for this will work? We've used a Shopify store before to sell retail, but if we go wholesale and sell to other stores, can we setup the app to charge the store owners for their product using the Shopify Gateway or do we need to have it set to use an external gateway?