Read a lot of general comments regarding operating a boat in rough water.

How would you handle your boat under these conditions.

Your direction of travel is West on main lake. Wind blowing across you at 20 mph from the South. Waves/chop at 3 feet.

Run in the troughs

Yes, run the troughs. Its not a steady speed. On and off the gas when you are in them.

This, but it obviously can change depending on the water. Best to just know your boat and do what you feel comfortable with and not try to rush.

Edit: BY depending on the water i meant that not all lakes shape up the same, such as boat lanes or hazards or even sea walls all around that cause waves to bounce back.