Ableton Live has a great feature where it automatically adds very small fade-ins and fade-outs to all audio clips. So when you are chopping audio in smaller chunks to resample or edit out the parts you don't like you are always left with an audio clip that doesn't cause clicks when played back.
Unfortunately, Logic Pro doesn't have the same feature. So I used painstakingly to add fades to every region using the fade tool until I discovered this great feature:
You can select multiple regions and add fades to all of them at the same time from the Region Inspector. You can even adjust the fade curves. This will save you a lot of time!