You can begin the PD process in a startup script. In most distros, I'm pretty sure this is as simple as modifying /etc/rc.local (see
http://www.raspberrypi.org/documentation/linux/usage/rc-local.md for more clear details).
Yours will probably look a bit different, but it should be pretty simple!
With Satellite CCRMA, you can also run the command "disable-flash-writes" before you set up your Raspberry Pi as an autonomous device. This will prevent data from being written to the SD card, so that you can unplug it without worrying about corrupting the SD card image. When you need to modify data on the card again, you can just SSH back in (or do whatever you normally do to control your Pi) and use "enable-flash-writes"
Let me know if you're confused on anything.
-Brian