i don't really understand what you mean by "from scratch". we arent really baking biscuits here you know, lol. anyway you look at it, you're going to need 3 things, a line out, an amplifier, and a decent bass speaker. in this case i think the easiest/cheapest solution would be to use car audio equipment. if you've got a little more cash to spend, there are some really nice powered subs out there for home audio, just plug and play if you go that route. check out some of the yamaha's and such they carry at best-buy. some great sound out of those and very easily adapted to pc use.
J.