Adding a Multi-Store to an existing store with an existing store. (Merging)

I'm pondering over adding a Multi-Store to my existing OC 2.0.3.1 store.
I have one problem with the path to take as the new store already exists on it's own website and I do not want to create confusion while I populate the new store within the Multi-Store environment.
So how can I do this merger without taking the existing store offline?