I use the spdif in / out hooked up to my PC sound card and then route the MPC out to my DJ mixer and / or PC through the sound card. I've never tried using the analogue in and outs, so I can't compare the sound quality, but I can certainly say that it makes for a very clean mixdown when you record the MPC direct to the hard drive on the PC. It's also good if you want to use your MPC in conjuction with some software (I generally slave ableton live's midi clock to the MPC and do the beats on the box and the loops on the PC).
The only slightly complicated thing I've had to do is to remember to sync the sample clock on the PC card to the MPC before I switch it on, otherwise you tend to get a nasty crackly mess of a sound when the two sample clocks conflict with each other.