Um, not true 5.1 as in 6 discreet channels, however Dolby dpl2 uses phase shifting to get a similar effect out of just two actual channels. Trust me, use the 5.1 track and let HB mix it to dpl2.
If you don't believe me, google Dolby Pro Logic 2 and see how it compares to simple stereo. Granted, the effect can only be heard when the iPod is hooked up to a surround sound system, but on the other hand, there is no real downside so why not let HB mix down the 5.1 to dpl2 in case you ever want to watch your iPod encodes on a bigger system. Hint: there is nothing magic about hooking an iPod up to surround sound, heck apple even supplies the necessary cables.