Heres a nice little "Cheat" I guess you could call it. If you dont want to waste time moving around the mouse and want to kill things faster, Pause the game, move the mouse over it, unpause, kill it, and rinse and repeat. I havnt goten there yet, but this might be useful at higher levels.
a quick hint for those that have troubles with ninjas: get a couple towers up front and a bunch in the back. when the ninjas first get hit they active thier smoke bombs and in 5 seconds they get past your middle towers. But it wears off near your gems. Your towers back there will be waiting to blast those mofos.