i had same problem.This is because if you use version 6.31 is when you have such file arrangements. Any how, this is the way i have done it.
1. update your version of game studio to the latest.
2. create a folder for your project in there.
3 create in that folder a project using WED and save.
4. in the map properties, select the option new, and for shooter game template.
5. go to project manager and add the template scripts for your new project.I am sure you know how to assign action to your models after this. then compile and run.
Hopefully this helps. cheers!
