they shouldn't be the same.

/etc/apt/sources.list should be empty (unless you really know what you're doing, and you manually added a repository there).

You should have several entries inside your /etc/apt/sources.list.d/hildon-application-manager.list. These entries will (should) coincide with what shows up under your Application Manager -> Application Catalogs.

example:

is the line that coincides with the "Extras" repository in the Application Manager.