How are you amplifying your speakers? Do you power them directly through your notebook or are you using some sort of an external amplifier?

are these your speakers?
http://www.avrev.com/equip/m&k/index.html

That klipsch probably isn't designed with your speakers in mind. My guess is that the lack of a proper reciever is the weakest link. Your right about the crossover point that may be a bit of an issue. your 2.1 amp may be underpowered or unable to really provide the juice you need to control your speakers.

I'm sure others have thoughts, I for one tried powering a set of Kefs through a similar sub/speaker computer system, it was absolutely awful.

I don't know what the sensitivity of those speakers is, but assuming its high, you may want to consider the sonic impact T-amp or super T-amp (30 and 100 bucks respectively) for an easy cheap solution. Given that your speakers have a bottom end of 85hz perhaps the regular t-amp would be in order.

you can find a review here on the stereophile site, and plenty others through google for that little amp.

cheers