Yeah, I can clear those questions up for you.
Like Mashiro said, we use Skype to talk to each other (or iChat if that week's third/fourth chair(s) use Macs), but it's not actually recorded that way. We each record our own separate track that only picks up our own voices. We clap at the beginning of each segment, however, which creates a spike in the audio. Then, in post-production, I'm able to line up these spikes so that everyone's in sync. That way, you don't get any of the lag or audio problems that come with recording straight off of Skype.
In case you're wondering, I use Audio Recorder for OS X for taping the show (since it's got low RAM consumption, offers monitoring, etc) and GarageBand for editing. As you might be able to tell, we are a mostly Apple family.