Hi Bob,
Thanks for the explanation on how the weighting etc works within the program. I was using my own weight to emphasize areas where alignment is most crucial when warping. When reading through the emask option and testing with the default .4 clip fraction from 3dAutomask I worried that one of the areas in the brainstem would be excluded that I am emphasizing, which is where my questions came from. When testing with the clip fraction of .33 (not realizing this is the default in 3dQwarp as opposed to 3dAutomask's default) the brainstem was covered and I reconfirmed this with the wtprefix option you suggested so it seems all this won't be an issue. At this time, I am aligning to a T2 weighted template space for some subcortical regions that are more easily distinguishable on this contrast as opposed to the T1 template.

Thanks,
Ajay