pickups with seperate outs.

No I don't have separate pick-up outputs, but I do customise my 6-strings a bit with switched pots, split humbuckers etc. On stage, these switches rarely get used, and I stick to the standard configurations.  
I would say if it's between you and your laptop, by all means go for it as an experiment.  However, the need for this is rather limited even for a six string where it probably makes more sense, and maybe some stage-stereo effects could be achieved. I think some Gibson ES-335 derivatives did this (ES-345, I think.  The "S" is not stereo in this case, but "Spanish", that's a different story). For a bass I would think the mod would be even more limiting unless you're going for some real exotic tonal variations, very melodic bass patterns, slap-bass, etc.  If I were you, when you have your soldering iron out, I'd go for a straight pot replacement for that errant tone control. It'll only be a few dollars.  But if you want to experiment with separate outputs, go the extra dollar for a stereo jack and replace your current mono jack.  All of this is only a few minute's job and completely reversible.  
 
Still, I'd be interested in what you do, and what effects you get.
 
Jerry

You don't see it done often, but it has become common practice to sample pickups separately in sampled guitars. Orange Tree Samples' Rick is a good example of what that does for you, and it's not just because you can emulate the Rick-O-Sound feature. I think the only reason it's not common practice with real guitars is the practical hassle of duplicate jacks, tone controls, cables and amplifiers.