With the iPod plugged in and the music paused, you should see an icon of a car at the bottom. See my photo demonstrating what to look for. Tap that icon and you'll get a menu of options for that input. One of those is "Autoplay" so tap that and toggle from "off" to "on". That should do the trick!
I've noticed that the Pioneer will only play back audio tracks in alphabetical order also when playing tracks off my SD card. Very annoying, I agree. I just tried with my iPhone and if I access my music using the iPod input selection, I do get my music tracks organized by track
