Are you using one of those blue anodized jigs from china ebay?
It took me a few failed attempts but I eventually figure out how to get good results.
I've seen some people on youtube that reflow with hte stencil in place, but I've found the same as you - mine warped with barely any heat and were useless in that regard.
1. Make sure you have a clean package put in the jig. Use some good quality wick to remove the old solder. Don't use crappy goot wick, I use MG Chemicals Superwick. It is imperative that you remove absolutely all traces of solder from the substrate pad. Use some rosin based flux.
They should be perfectly flat with no burrs or bumps.
http://imageshack.us/a/img801/7411/gzhp.jpg2. Sometimes you may have flux residue that causes the pad to be dull, and it won't react to the wick. Use a blunt xacto tip or a dull knife tip the carefully scrape off the excess residue and re-wick.
3. Clean flux residue with a microfiber cloth and 91/99% isopropyl alcohol.
4. Align the jig and stencil. You'll notice the top 2 jig frames that sandwich the stencil are very subtly marked with a dot in one corner, to match the base. Tighten all 4 stencil holder screws in a star order, then loosen just enough so that the stencil moves freely.
5. Use some sharp tipped implement to push the stencil around so that it lines up with the package underneath. Look down directly over it to eliminate parallax error, then tighten in a star pattern.
6. Pull off the stencil frame, noting which way the key is. Apply a small amount of flux (I use a rosin flux pen, MG Chemicals 835-P, do NOT use noclean or water soluble fluxes) to the package. The flux I received with my jig was a gloopy thick one, and while it worked, it was so thick the balls would float around in it and borg with neighboring ones while melting.
7. Replace stencil frame, put on balls. Mask off the unused areas of the stnecil with kapton tape. You can pour hte excess balls back into the tube if you're careful.
8. Have reflow oven ready to go. I used a bog standard leaded profile because I have leaded balls.
9. Now the tricky part is you need to lift off the stencil and carefully take out the package itself from the jig (the jig soaks up too much heat and causes incomplete reflow), put the package with placed balls on a carrier pcb. I use a spare unpopulated pcb for this. Then it goes in the oven.
10. Reflow
http://imageshack.us/a/img850/2060/hb6k.jpgDon't put the jig in the oven like I did, it took two runs to get the heat up high enough.. by which time your flux may burn off.
Here are a 0.8mm BGA I transplanted with this method, and another 1.27mm pitch graphics asic I reballed as a test.
http://imageshack.us/a/img17/1203/9qs2.jpg