Public App Installation Process

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Hi Shopify Experts
I need general information, when an app is installed form marketplace. How the API & Secret keys are generated and stored to generate access token for each store.
I have created an app from partner store and and save API & Secret keys in a text file on an external server. I have put all my php files on externail server to create snippets, liquid files on store and show some contents on store's front-end. I install this app on development store using URL
on redirect page I then use these API & Secret key with api url admin/oauth/access_token to generate and save access token for my development store.
I have a question here, when a merchant installs an app from marketplace how API & Secret keys of this merchant are stored to generate access token until merchant share its API & Secret key with app owner manually to generate access token.
Please elaborate me at this point w.r.t to my manually installation process and marketplace installation process regarding API & Secret keys.

Please mention if there is inconvenience in understanding of my question.