Get The Vertical Lines

For the next step a 4' level is very handy, you could also use a chaulk box. What you have to realize is the possibility that your roof joists or trusses were not exactly put in perfectly. With that in mind, use your level to draw a line from the end of one line, to the end of the other line. If you are using a chaulk box, drive a nail in the end of the line and hook onto that. Then hold the string tight at the other end and snap your line. Now use your framing square to see if everything is square. You should also notice that the line goes down next to the joist or truss and is fairly even all the way down. Now mark the other end in the same way and you should end up with a rectangular shape (or a square if you're installing a square skylight).
When you go up on the roof, you'll need to be able to find this location. Drive a nail up through the roof at each corner. Then get a carpenter's crayon, your saw of preference (circular or jigsaw or both) and a straight edge (4' level) and head up on the roof!

On The Roof

Make sure you are doing this on a day that does not call for any chance of rain. Also, be sure you start early enough so that you can finish before dark.
Locate the nails. You can pop them back into the attic at this point. You'll want to remove any shingles that are in the general vicinity of the skylight. At least two courses above the light, 18" on each side, and 18" below. If you use a fork tool and a hammer, you can probably remove the shingles without damaging them. Then you can reuse the same ones to put back on. If you get up on the roof early, or it's a cool day, you can pop the bottom edge of the shingle up enough to get to the nail that holds the lower shingle in place. Usually there are four nails per shingle. Don't cut any shingles at this point, the dimensions I mentioned are just the area that needs to be cleared away, you will likely clear a larger area in some places, due to shingle placement because the entire shingle has to come off. This will also mean that you have to take a shingle off that is outside the dimensions, just to get to a shingle that is inside the dimensions. That's life, don't whine about it. You're not the first person that had to do that, trust me.
You should be able to tell which holes are for your skylight, if not, have your helper go back in the attic and poke them through again. Measure the dimensions again to make sure you do in fact have the right holes and that you did, in fact, measure right the first time around. Use your crayon and straight edge to draw a line on the felt paper to connect the dots. You should be left with a rectangle or square. The next part can be tricky if you've never done it. Retract the safe guard on your circular saw and position it right above a line, at the corner. Turn the saw on and slowly let it down into the roof (I'd have a junk blade on it before you do this, cause you'll have a junk blade on it when you're done). Keep the front of the shoe (the flat plate that contacts the wood you're cutting) pressed against the roof to help prevent kick backs. This is called a plunge cut. Once you're through the roof, follow the line to the next corner. Repeat the process at all corners. Be sure you DO NOT cut past your marks, and do not rip, tear, cut or otherwise deface the roofing felt.