I recently bought the z-5300's and an audigy 2 ZS sound card. I like the speakers a lot. When you heard them at the store i'm guessing the sub was right next to the speakers and on a shelf about chest hight? Thats how i usually see them setup anyway. with that setup the bass is going to be a little much because the sub is usually right by your ear. When they are in my room i turned the bass all the way down on the remote and it sounds pretty balanced. Putting a sock in the port would kill the bass. The subwoofer is a bandpass design meaning teh only way bass gets into the room is through the port

. If the bass is still too much after dialing the bass back through the remote you can always pull the sub out form the wall a few feet.
For games these are outstanding performers. Especially with the audigy sound card. I went from headphones to 5.1 and for first person shooters i'm never going back. having 5.1 in games is a great improvment. You can hear whenever someone is coming up behind you and you can hear were other people are. The bass is boomy but for games i think thats a good thing. I like to have a nice boom when the nades go off

. Now to be fair the bass isn't much boomier than any other computer speakers i heard including the Klipsch speakers in the same range.
As for the MP3 thing heres how it works. The speakers come with 1/8" interconnects. One for center/sub one for left/right speakers and one for left/right rear speakers. They go into the three 1/8" jacks on your sound card. and into the three 1/8" jacks on the back of the sub. When you play an MP3 (as long as your not emulating 5.1) the sound card should only output sound in the 2 front channels and the sub channel. Or at least thats how it works with my audigy. I shopped around a bit and I was deciding between the cambridge megaworks 6.1 and the logitechs. Unfortunately i couldnt hear the cambridge so i had to go with the logitechs. Part of the problem with 5.1 computer speakers is they wont have the same quality sound as good HT speakers. So you can spend a lot on computer speakers and the performance isn't all that much better than the z-5300's. That was my conclusion after hearing the Klipsch ultras and the logitech z-680's anyway.
Ryan