A project can have multiple target configuration files associated with it, but only one will be "Active". It is the "active" one that will be launched when you click on bug button (debug active project).
This wiki page touches on it at step 5:
http://processors.wiki.ti.com/index.php/GSG:Debugging_projects_v5#Creating_a_Target_Configuration_File
Does this answer your question or did I misunderstand your question?