To interface STK with another application, various options are available, depending on, among other things, the type of task involved (analysis only? analysis and visualization? playback visualization?), the type of client application (MATLAB, custom applications, MS Office, Web browser, etc.), and the environment in which you will develop your application (including STK MATLAB, the COM Interface to STK, the Viewer Control and Viewer Application object models, and a number of different Connect libraries).
A clickable decision tree provides an overview of your options.
STK Programming Interface 11.0.1