You could alter the bass and treble with an equalizer in the system, maybe? But my suggestion is to let the next playback unit (car CD, component system, computer audio) be the point of alteration. I'm not familiar with the software or plug n play devise you're using. I snagged a copy of Cool Edit Pro a few years back off eBay and use the native sound card in my computer for audio work. There are many adjustments for all sorts of effects once it is digital in Cool Edit. Another choice that I'm not familiar with is Audacity (open source freeware at SourceForge). I've just never used it.
I wouldn't be using auto leveling at all. More than likely that is where your clipping originating. I've done very low level input (via control panel>sound>record level) with excellent results. In the end, before making a final copy, I do have to boost the audio levels. But zero clipping has occurred to me at very low levels and I can control the amount of db boosting so that high end clipping doesn't happen.
OMG, that deviant Microsoft player! That's all I would use it for -- playback only. The last time I tried anything else was burning a CD. I felt like I was on a trip from Chicago to New York with stop overs in Omaha and Miami. Disc burning works very well with Nero. I've made about a hundred or so that way. You could try out winamp or audio catalyst. I just found a copy of Realtek player on my computer. It does have a 10 band equalizer on it. Must have come with the motherboard on the last rebuild.
Well, that's my ten cents worth...