In my opinion you need both a roofer and carpenter.

I had skylights (Velux) installed as part of a new roof in 2003. Most
good roofers are familiar with the flashing procedures that are
required, and most will also guarantee their work for a period.
However, I had a good carpenter do the interior framing and insulation
once the skylights were in the roof. Insulating the shafts is important
to prevent ice damming.

I had them installed on the north side of my house, and it changed it
from dark and dreary to bright and sunny.

Ask the roofing to use a waterproof membrane, which isn't required, but
not a bad idea.