Competition template

Question: Is it absolutely necessary to use the competition template?

I have a pair of students whose autonomous and driver control sections will work together in a normal RobotC file. When it is placed in the template, the autonomous section will not run.
We have commented out the autonomous code, inside the template and the driver control portion works fine. We have commented out the driver control section and the autonomous portion will not run, while it is in the competition template.