For me, I just take a hose and some simple green/purple power (same thing as simple green). I give the engine compartment a good washing, then spray the simple green, and finalize it with a good rinsing. I close the hood and proceed to wash the car as normal. When the car is washed and dried, I'll pop the hood back open and dry the engine compartment (whatever I can reach under there) with a cotton hand towel. I also use a couple cotton hand towels to dry the inside of the doors, hatch, and the door sills. And when I wax the car, I'll sometimes take Back to Black plastic wax to the black plastic pieces under the hood.
Also, my dad has a CAI in his Camaro, and had one in his G8. Anytime he washes under the hood of those cars, he'd uninstall the filter, put some foil over the opening of the pipe, and secure it with the clamp for the filter.