Pretty broad question, but there a couple of standard fixes for this set up:
1. Make the left sidebar resizeable
The left sidebar is a common pattern for users. When confronted with a main panel that can be heavy on information, users often instinctively try to resize the width of the left panel as needed. Be sure to store their adjustments so they hold next time the app is launched.
2. Offer full screen
Once the user has the filters and view preferences set for the main panel, they're ready to dive into the information. Allow a quick switch to move all the controls out of view to maximize the viewport.
As for left vs right, it really depends on what your users are comfortable with. Is there another application they use that makes you think right is better? Have they asked for it? I would say that filters on the left is more common in general use, but this seems like a niche product.