good question, surprised it hadn't gotten a response.
Barring technical quality issues, I'd go with Roll20 instead of Skype. last i heard, Skype didn't do multi-party conferencing for free, roll20 or Google hangouts does.
Also, Roll20 has the gaming tools built in and it is built to be VERY easy to get started with all your players. That lowers the technical skills barrier to entry that may exist for some of your group.
Some generic advice:
Take some lessons from folks who conduct teleconferencing.
put everybody on their own computer so they can all see and use their same interface. Do not put half the group sitting in the same room as the GM, and the other half at remote sites if you can help it. Otherwise, the kids in the room with the GM will dominate his attention and the folks in remote sites will feel neglected.
Make sure everybody is prepared to listen for audible cues that somebody else is trying to speak and to BACK OFF to let them speak. The GM may need to verbally indicate, "Bob, what were you trying to say" which means everybody else needs to shut up. For the most part, teleconferencing is half-duplex, which means that literally, only one person can talk at a time. Even with a full-duplex system, you trying to interject will mess up the audio badly for everybody.
Speak clearly so that everybody can hear, despite some interference in the signal. The internet operates on a non-reliable protocol, which means that moment to moment, your voice packets are traveling at slower/faster speed. VOIP is not crystal clear.
The GM should do a practice run with the tool for a few encounters to see how the map and tools work. This should just be a test. Use some goblins and a 1st level fighter PC. The goal is for the GM to be comfortable with the tool, not to actually play the game on this test run.
