Welcome to the Cove. In short, QS9000 is the automotive flavor of ISO9000. The Big Three (Ford, Chrysler, GM) have created a document consistent with ISO standards (the foundation) and have added the automotive requirements. The common elements between the three are inclusive in the automotive flavored ISO elements (1994). Where they couldn't agree, they have created the Customer Specific addition to the standard.
I would recommend a search of the forum (use the search tool here in the Cove) to find out more. Marc has also posted several pdf files that might interest you.
Kevin summed up the differences between ISO and QS pretty well. In effect, QS is the automotive interpretation of the ISO (1994) standard. Where ISO allows some latitude in an implementation, QS is more directive.
As for TS 16949 replacing QS-9000, I believe that will be the case. Effectively, the Big 3 will already accept TS registration in lieu of QS, and AIAG has indicated there are no revision plans for QS to align it with ISO (2000). The TS is slated for revision to align it with the new ISO revision.
That's not to say you'll be able to ignore AIAG publications. The customer specific sections (Section II of the QS manual) are still invoked by the Big 3. And they'll still use the PPAP manual as their customer specific production approval process.
In the long run, I'd suggest pursuing registration to TS if you're just starting out. Of course, that's if you service the auto industry and are getting pressure in that direction. If there is no firm pressure towards automotive interpretations, it's entirely possible a straight ISO registration is the way to go on the front end. You can always upgrade later.