How can I best integrate a complex payment system with an app on Shopify?

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We are creting a app , which is free for 1 week , then if coustmer suscribe , n tokens are given to him for a month to use. but sometimes they need more than n token , and for that we have in app purchase. now we are confused on how to integrate this with shopify. We already have our app on lightspeed and other platforms and we have a inbuild shop product they buy. whats the best way to do this in shopify.