I can't speak for anyone else, but I paint the highlights and shadows on, no filters or automatic effects. As long as you keep the internal structure in mind and put your dents away from panel overlaps, stringers, formers and bulk heads, you'll be ok.
But whatever you do, keep them subtle
Here are a few pictures to illustrate how a simple fuzzy shadow and fuzzy highlight in combination will do wonders;
Smooth, no dents-

Dents but with the detail removed-

all together-

The final product-

(That reminds me, I've really got to do a new profile some day

)