I haven't really messed with crossovers on soundcards since I haven't really had that option and have been using a digital connection for several years. A crossover frequency usually means that below whatever you set it at, the signal starts to get diverted to the subwoofer.
For example in a movie you might have 5 tracks for the speakers and 1 LFE track for the sub. The really low effects tend to be on the LFE track (low frequency effects) but the other tracks also have a good deal of bass in them.
Unless you have speakers that are fullrange (like good response below 30hz... and even then it would be questionable), you'd want to set your crossover frequency and run the speakers as "small". In hometheater applications, the standard setting is usually ~80hz. With that setting, bass below 80hz in the tracks for the speakers starts to get diverted to the sub. This isn't a brick wall where it is all transferred, but a gradual transition away from the speakers. If you set it to 80hz, you'd want your speakers to have good output to about an octave below that... 40hz in this case.
I don't know why I'm saying all this except that I don't quite understand why setting the crossover higher is reducing the bass. Setting it higher would just seem to be causing more signal to get to the sub and would tend to make it produce more sound. The issue with computer speakers is that they already have a built in crossover that's designed to match the capabilities of the speaker set. Since computer speaker satellites are usually very small and incapable of producing bass on their own without... well... destroying themselves, the subwoofer crossover is usually set pretty darn high.
That's part of the reason why subs in computer speaker systems tend to be annoying. If you have a relatively powerful (or loud I guess would be a better word) sub, it ends up blaring some of the frequencies above 80hz. Not only can you localize where the sub is since the crossover is set high enough that the human ear can locate the higher frequencies coming out of the sub, but it tends to sound bad in general
Because computer speaker sets have a set crossover point built into them, I'm not quite sure what setting a crossover in the signal you give them is really doing. For small speakers in hometheater applications, 200hz would be quite high for a crossover point. If you're setting your to 400hz or higher, a ton of frequencies would be getting diverted to the sub. Depending on how the "crossover" really works though, I could see how that might actually be kind of like a high pass filter. Maybe the information below the "crossover" frequency just gets thrown out. That would certainly explain why setting it higher would reduce your bass output.
If you want to get nerdy, you could try to get some test tones and listen to some different frequencies and try to tell what is really going on.
At any rate, I would think a decent equalizer in combination with setting the sub's volume control all the way down would be enough to cut the bass down on the speakers. In my own experience with the cheap logitech sets, turning the volume on the sub all the way down was enough to get them tame enough. Add to that a possible 20dB reduction to bass in equalizers, and I have a hard time believing that you really need to mess with "crossover" controls.
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