Well, first of all, you will always lose AF on a non-1 series body with a 2x TC on any lens that is not at least f/2.8 or faster. That's not a problem with the teleconverter, that's a limitation of your camera. Non 1 series cameras can only use AF on lenses f/5.6 or faster...and if your zoom is, say, an f/4 to f/5.6 aperture zoom, it'll be f/11 at the long end with a 2x...not even my 1Ds Mark II will autofocus at a max aperture of f/11.
Teleconverters are not made for lenses shorter than about 100mm, so it's no wonder the 50 looks like crap with it. That said, a 2x TC is also going to have pretty severe image degradation on all but the very best lenses...there is no free lunch. Now, I don't know what TC the Quantaray is a clone of, but it is likely a Kenko or Tamron clone...if it's a clone of the Pro Kenko, it's actually a pretty good TC...but you won't be able to see it unless you try it on a piece of very good glass, such as the 300 f/2.8 or 200 f/2.
Stick to a 1.4x TC for most lenses, and I'd frankly avoid a TC altogether unless you are using very good lenses, as the image degradation will be too great. The 70-200Ls (all of them) take a 1.4x TC pretty well, but that's a starting point. If you've got a cheap consumer zoom, forget using a TC.