When running through the earlier stages, it is actually more beneficial to either sure-aim with
or just try your best to be precise normally with the right stick and dislodge the enemy heads as quickly as possible. It takes fewer shots to remove the head than it does to destroy the body. I wouldn't worry too much about this early on as you will encounter hundreds or thousands of enemies to practice this on. One choice location in particular starts from the Power Dome and proceeds through to the Grid Clash arena. Going through the Power Dome, you'll find that many of the Shepherds respawn to hinder your progress through the shafts. Furthermore, the Grid Clash seems like it is an endless spawn-point for the main field (unless it loses power when you proceed past that point).