If you use bridges and cut them away after you apply the important parts of the stencil to the shirt everything should stay together.
Here's a good island/bridge tute:http://img312.imageshack.us/img312/8726/islands8qc.jpg
Also, instead of drawing directly on the freezer paper I print out my stencil on regular paper and cut it out with freezer paper underneath. Its best to use a sharp exacto blade.
I hope this helps!