This video shows you a quick way to clean your audio tracks with Strip Silence. This removes areas where the audio is not playing anything (although there still may be noise or hum from instruments).
This video shows you how to line up your project in Pro Tools to a Metronome using Identify Beat. In other words, you will Quantize the grid to your performance instead of the other way around.
This video demonstrates how to turn down the volume across your whole project even when automation is written on your tracks.
How to Quantize MIDI in Pro Tools by applying the quantize directly to a MIDI clip. This video also explains how to restore the original timing of a performance after a quantize has been done.