First, I am not a linux power user. I have used it on and off for several years and only this year have I switched 100% over from Windows. I have recently gotten into podcasting and I wanted to be able to record my skype calls. This board helped me do it with the skype-rec program, and its fantastic for post production, but I wanted to do a live recording using Jack to cut down on production time.
It took me HOURS to figure it out, but I finally have a working solution. I hope that this post will put you on the right path because I had to learn a lot about linux in order to get all the modules working. Here is what I discovered in the process. Your distro will be different and there is no guarantee this will work on your setup, but at least you will have a direction.
1. This first thing you need, of course, is to make sure Skype works. I assume this is the case. No crackles, no hisses, no mickey mouse affect. My skype has worked flawlessly and the sound quality for recording is outstanding.
2. Make sure Alsa is configured correctly. Go to the alsa home page for tips. Read the section on using the asoundrc file. This isn't essential for Skype but it helps in your understanding of the Linux Sound architecture. Before this, I had no idea what the difference was between Jack, Alsa and OSS. Now I do.
3. Install Jack. Do it from source so that you have all the development files for other applications to use. This will help if you need to compile Arts from source with jack support.
Make sure jack is working and also make sure you have it outputing to the alsa driver, not the oss. Our goal is to avoid oss completely. This may not make a difference but it allows you to manipulate your audio streams for any future use using the asoundrc file.
Gettng jack to run is a major hassle. When it works, it works great, but you have to do some major work to get low latency performance. For me, it was a ton of trial and error, but here is what I use for jack.