Custom Application - Noobie

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I am brand new to Shopify.  I am not a merchant.  I am a developer.  I do not own a store front other than a test one.


I have been tasked by my employer ( a fulfillment center ) to write a Coldfusion application residing on their server, that in their words "will integrate with Shopify".  They are envisioning the end result to be such that the application I am writing, while residing on their own server, will be visible and usable from within the store owner's apps page.


I am familiar with using a private app's API key to make calls from my employers server to the store owners Shopify account ( in this case, my own test account ), but it seems they want it the other way around ... from the store owner's admin to our private web server.  They expect to see the interface I built on our own server to show up within Shopify. 


I'm confused and have no idea how to do this, if indeed it is possible.


Can some kind soul please give me definitive instructions on how to accomplish this?