Hey there SoSimplified! I might need a bit more clarification in order to help you out.
Why are you trying to only utilize the Billing API with new customers? Is there something missing from our APIs that you require for legacy work?
And is your question about how you might keep track of only new merchants? If so, this is a bit of a tricky problem, explored a bit here: https://community.shopify.com/c/shopify-apps/distinguish-callback-url/m-p/779649 It looks like your best strategy might involve adding some logic to assume a store was already installed during the callback if it exists in your DB and has never seen the uninstall webhook hit for it.