I clean the engine compartment every other time I wash the car. Leave the hood up for ~10 mins first, and then use a light cleaner like Simple Green or if you're at a self-service car wash, use the Presoak. Then rinse it. I use the high pressure spray but do it from a few feet back so it's not so focused.
I have a "third" chamois that I use for drying the lower body cladding and the engine compartment ("first" and "second" chamois are for glass and paint, respectively).
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