Generally speaking, you should confine most of your processing to the mid view. In this view the filter changes you make are applied to both mid and side channels simultaneously which is equivalent to applying the same filter response to both channels.
Left and Right views are typically not used for editing except in special circumstances or for an effect.
The side view you can use to alter the stereo image of the track. Boosting levels will widen the stereo image and cutting will narrow it. A commonly useful usage of the side filter is to monophy the bass by applying a low shelf filter with a knee at around 300Hz.
You can easily delete the files created by Har-Bal after each project completion by clicking on File/Close and the File/Manage Files delete.