I've been doing this very thing today, having finally bought a good gun vise and built a rock-solid bench for it! I shot over 200 rounds from my new rifle before I started to think about filing, because I felt I needed to shoot it in, become confident with the mechanics (being new to flinters) and get the right ball-patch-load combo. Mine was shooting low too but I just concentrated on the grouping, and now that I'm satisfied with that I'm filing after each five rounds and watching the group slowly rise up the target.
I settled on 50 gr 3F, 440 ball with 015 patch for my 45 cal, so maybe you would need a bigger load as someone above suggested. Also I'm zeroing at 50 yds.