I am having some difficulty using PID on my flywheel motors. The wheels start up smoothly but then they significantly decrease speed. When I launch a ball through, they increase speed a lot but then go back down.
I would greatly appreciate some help.
PID is one area where it is very difficult to give advise without a complete understanding of the robot design. I suggest you start by reading some of the existing threads that are discussing PID, here are two good ones if you are using your own PID control loop.
This one discusses using the internal PID that ROBOTC V4 contains.
If you then have specific questions about implementation details feel free to start another thread.