This certainly sounds like a good experiment and your description of the test setup
appears to be sound and well thought-out --
For purposes of hypothesizing possible test results, you may want to take a look
at the physics aspects of this special case, ballistic flight dominated by aerodynamic
drag and weight. The "ballistic coefficient" is an engineering parameter, weight
divided by the product of drag coefficient times surface area. A writeup on
ballistic coefficient:
http://en.wikipedia.org/wiki/Ballistic_coefficient
In your test as described, it appears that drag coefficient and surface area will be the
same, or very similar, for the two categories of pellets. Pellet weight will thus be
your primary independent variable. A reasonable hypothesis for you to consider,
based on ballistic coefficient explanations, is that the heavier pellets will accelerate
faster and maintain velocity longer, resulting in shorter flight times to the target.
But will your test results support this hypothesis, based on your particular test setups,
that is the question - and the challenge!
It may be worth measuring the error distribution (miss distances) as the pellets hit the target -
you may find that the heavier BC pellets have a tighter shot pattern due to their higher
velocities.
Speaking of other possible error considerations, be aware that manual stopwatch measurements will
introduce a measurement error, and you should take this into consideration when evaluating
your experiment results.
Good luck with your project, it sounds like you'll be able to make some interesting observations!
Peter Young