Whether you attach directly to plywood or add a foam base or roadbed:
1. No need to screw every piece down - one every 3-4 sections depending on size and location is generally sufficient.
2. I avoid screwing switches down.
3. If the screw head sticks up too far, use a small countersink bit to slightly enlarge the hole so the screw sits down in the hole without having to overtighten the screw.
4. Do not overtighten.
5. See # 4.