Well, the empeg isn't as many other headunits preboosted in the bass department, instead it is flat. There is the equalizer that you can tweak the sound with - I'd recommend cutting the highs rather than boosting the bass - less risk for clipping.

Reading mp3s back to the PC: the latest beta of emplode will let you do that, as well as jemplode (3rd party thing)
Your player shipped with 1.02, latest stable release is 1.03 - definately upgrade to at least this. It's available here.
Latest beta version is available here.
Always first upgrade the PC software, then the player software. You need the same version of PC and player software as not all versions can talk to each other.

jemplode is available here. I think you need the latest beta of the player software.

Most, if not all, of this is answered in the FAQ, do take the time to read through it. Also check out the links that are at the top of every page of the BBS.

/Michael