Garrett started a podcast running through Audio HiJack Pro on the Mac. They've now decided to record locally at each end, though. Leo says that's called double-ended recording. Leo doesn't do that because it's a big hassle due to latency. If it's done right, it can sound incredible, but it's a lot of work and takes time to get it just right.
If he wants to use the double-ended recording technique, he could use a clapper board or just a single clap to the microphone to get the tracks in sync. Then he can just line up the clap spikes in the audio waveform while editing and he'll be in sync. Over time, it'll slowly drift out of sync, so about every 25 or 30 minutes he'll need to clap again. It would be better to make sure everyone has quality mics and have each user talk on a separate computer that feeds into a mixer.
He can also improve Skype by making sure everyone has a good connection, and all have good mics such as a Plantronics headset mic or the Blue Yeti with a USB connection. He can use Netalyzer to make sure his connection is sufficient.