If you use Skype to bring in audio from a co-host or a regular guest, are you having problems with Skype "ducking" the audio during the call? That is, when the guest and the host talk at the same time, is the lower volume audio suppresed in favor of the louder one?
The reason you have the issue is Skype is a half-duplex communications system. Only one person can talk at a time. While Skype does a great job of balancing the callers, if you as the host try to play music over Skype for your guest, such as theme music, the ducking problem will become blatantly obvious.
There is a quick solution. Take a look at this article on the IAIB (and become a member.) If you have any questions or comments, you can reach me on Twitter (@mcphillips) or in the Podcasting Technology Resources Community in Google+ Communities.