Mac Mini configuration

I suspect this has been addressed; if so I'd appreciate a link. This will be my initial step into computer audio.

I have a Mac Mini running Mountain Lion (OS 10.8), Musical Fidelity USB-S/PDIF converter, and Pure Music. A couple of questions: Should the output of the USB-S/DIF go to my Oppo BDP-95 or directly to my Cary Cinema 11a processor? I think the Oppo has 32 bit DACs, the Cary 24 bit DACs, both likely 192 kHz. How much, if any, of the application software that came with the Mini should I strip out? At some point the USB-S/DIF will be upgraded, but at $100 it seemed good value for a beginner.

The rest of the music system is Proceed Amp2 and 3, KEF R107/2s with KUBE, KEF R102 centers and surrounds with KUBEs.

Doesn't matter. Try it both ways and see if you can hear any difference.

Some people have all kinds of ideas for modding the mac mini - new power supply, solid state hard drive etc. Strip the software down to the basics needed.

Again, play around if you like - I run mine stock and am very happy.
Do yourself a favor and google Empirical Audio. The information found there about setting up your Macmini is spot-on.