Often System Generator is used to implement a portion of a larger design. For example, System Generator is a good setting in which to implement data paths and control, but is less well suited for sophisticated external interfaces that have strict timing requirements. In this case, it may be useful to implement parts of the design using System Generator, implement other parts outside, and then combine the parts into a working whole.
A typical approach to this flow is to create an HDL wrapper that represents the entire design, and to use the System Generator portion as a component. The non-System Generator portions of the design can also be components in the wrapper, or can be instantiated directly in the wrapper.