Using a template is not going to improve your stitch, in fact it will probably make it the parallax seams even more visible.
Autopano Video uses the overlapping content between each video to automatically create a 360° projection. So in a way, each time you import all the videos, synchronize, and stitch; you are effectively creating a custom template that is optimized to that individual shot and its specific parallax errors.
Due to the unavoidable parallax errors, you will get a much better result if you do not use a pre-made template. There is no such thing as the "perfect" template, since all of the camera sensors are not at the same nodal point.
Pre-made templates are especially ineffective now that in AV 3.5, you can interpolate between different stitches.
If you are having problems with AV recognizing one of your channels, make sure you are selecting a good frame in the timeline as your initial stitch. But occasionally a shot pointing straight up at a blue sky will not automatically be placed for stitching and must be placed manually.