Shopify App Subscription Payment for a Public App

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I have a public application, approved for Shopify App Listing. Initially, we offered an app with only a free plan, but now we are planning to open our paid features for the Shopify stores that install our app, and for that we want the payment procedure to go through Shopify.

The paid feature will have a monthly fixed cost let's say $5, which will be collected by Shopify (I assume) plus additional charges for extended features with the same plan. These payments will be monthly based and for additional charges, we will provide Shopify the base to score the total cost, let's say 10 mins with the rate of (0.01$/min) then Shopify will need to get $5 + $0.1 (0.01x10) = $5.1.

However, we having some concerns understanding how is that achievable and which APIs will be used to provide Shopify details about the store usage and amount to be charged.
Is there anyone who knows how to deal with this case scenario?