the fenders should be off for paint. The box would need to be off for the painter to paint in between the box and cab. the wood should be installed after the paint.
who does what is between you and your painter, I would have him do the technical stuff or things that you are not comfortable with.
It really comes to your budget and how much you want to do too.
that being said; there really is no rule to how a paint job is done. It depends on what you want; the important thing is that your painter understands your goals and your budget. Generally speaking a color change takes a little more effort as the jambs door etc should be done too.
as far as black goes; mine is dark gray(almost black)-it takes a little more effort to keep it clean-but this truck is a weekend cruiser and something to take to the local car shows and have fun with it. everytime I take it out it pretty much gets a good dusting and fingerprints cleaned up bugs cleaned off etc. It does get a little old cleaning it all the time, but I imagine I would probably still do it no matter the color. Also waxing takes more effort as swirl marks will show up a easier on a dark color and that to me is the biggest downside to a very dark color, I wouldn't hesitate to paint it the same color if I were to do it again.
As far as that goes my work truck is black-I would not get black again for work.
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