Audio can be extracted both ways, via IDE or the analog cables.
In Musicmatch Jukebox (7.2 in my case) if you look under Options-->Recorder-->Settings you'll see "CD Recording Mode". The default is Digital, no error correction. The other options are Digital <b>with</b> error correction and Analog.
I too had glitches (sounded like ticks on an old LP record) with my old sound card (an ISA one). I learned that under the sound mixer if I disabled recording from all sources (line, microphone, CD [analog], etc) except WAVE then the glitches were eliminated.
<b>56K, slow and steady does not win the race on internet!</b>
1. I have used the digital connection between the CD-ROM drive and the sound card and it works quite well. If for whatever reason you don't want to enable DAE (Digital Audio Extraction), it's much better than the analog connection because in this case, you will be using the much better Digital to Analog converter of the sound card rather than the [normally] shitty one in the CD drive itself.
2. Ripping audio from CDs has nothing to do with your sound card. You can have a system without a sound card and still extract tracks from CDs. The process is an all-digital one and it's done through the IDE cable (a better way to put it is mentioning the PCI bus, the CPU, etc.).
If you're hearing clicks in MP3s, you have to check a few things. Does this happen on every CD? If the CD drive is not reading the tracks correctly this may happen. Enable Error Correction on your ripping program and although it may take much longer to extract the tracks from the scratched or other problematic parts of a CD, it is much safer. Also (and this is very important) what is your encoder (for converting the WAVE files extracted from the CD to MP3 format)? The quality of MP3s extracted by the Xing encoder for example is awful. Check to see what encoder the Music Match uses. If it supports external encoders, download and use LAME. It's the best you can find.