Well, since the world of Shadowrun is pretty much a modified version of real life (and that's why I love it) you could treat an SR bounty hunter just like a real life bounty hunter, i.e. your job is to track down individuals who have been arrested and released on bale, who then "skipped town" without showing up at their trial. I know that might sound a bit fraggin' boring, but think about it like this, in the world of Shadowrun, there are a TON of borders in the world that a person might cross to evade the law. Imagine you have a few Mitsuhama sararimen (wage slaves) go out on the town in the middle of teh Seatle Sprawl. After an evening of drinking and partying, they end up in Auburn and hire a few caucasian hookers for a bit of color and things go south. One of the hookers ends up dead, the sarariman gets arrested, and by some freaky legal loophole, he makes bail. The guy then goes into ANY Mitsuhama building, and is now in Corporate territory. If Mitsuhama has no extradition treaty with the UCAS, then Joe Corporate is on easy street.
So you could work a boutny hunter like that: a guy who has a quasi-legal status which allows him to track and bring in bail jumpers or fugitives on the run. I know the above example is a bit of a stretch, but you get the idea. But you have to remember, a REAL bounty hunter has to work within certain lawful precepts. So if you create a PC who is a "real" bounty hunter, then he should probably have a SIN and a business liscence. If you are a "street" bounty hunter, then you could probably run it the same as in Star Wars.
Gabriel