Remember that the way you cut the ceiling depends largely on what amount of light you want in the room. A larger opening requires careful planning, but isn't much more difficult then a 'straight down' opening. I'm going to be describing a straigh down cut, but most of the same procedures apply to an angled opening.
I like to go in the attic and use my plumb bob to mark down each of the other three corners (you should already have one hole marked, unless you had to move things around). If you are dealing with conventional rafters (as opposed to trusses) you'll also have to contend with the offset. This is typically dealt with by placing the skylight up against the correct rafter so that the jack rafter on the other side will line up with the ceiling joist below it. Drive a nail down through the ceiling and then go down below. Draw or snap a line from nail to nail. This is your cut line.
Use a reciprocating saw and be sure to have goggles and a mask on. Again, be sure a large tarp is down and covering anything you value. I'd even cover things that aren't near the 'danger zone' to prevent dust from getting all over them. Also shut any doors and open any windows. That will keep the dust confined to inside the room, and out the window. If you encounter a ceiling joist, you'll have to angle your saw so that you don't cut through the joist, just the ceiling. Depending on the size of your skylight, this piece could be large so be prepared to have a helper ready to support it while you cut. The corner of a 10 piece of drywall from 8 foot high does not feel good on toes.
Like I mentioned before, if you have to cut through a ceiling joist (i.e. a large skylight) post on the forum and I'll tell you what you have to do before you start hacking away.

Framing

Since you used a plumb bob you're probably real close to being in the right location, but I like to double check with a level. Take it from the face of one of the headers on the roof and lay it up against the ceiling joist. The flat side should rest on the ceiling joist. You're not seeing if the rafter and ceiling joist are plumb, per se, you're going to set the level plumb and put a mark on the ceiling joist. Repeate this at every corner so that you have a good, accurate location for the headers on the ceiling.