When you use the Manyshot feat, you can fire each arrow at a different target instead of firing all of them at the same target. You make a separate attack roll for each arrow, regardless of whether you fire them at separate targets or the same target. Your precision-based damage applies to each arrow fired.

Furthermore, a cumulative penalty for firing more than two arrows are reduced to -1 instead of -2 (-4 for two arrows, -5 for three arrows, etc)