I look at it as if the brain is malfunctioning and sending out bad signals. These signals are carried into our thoughts and with the illness they can be twisted many ways. The medication (once it is balanced right) works to make clarity of the signals and clears all the excess muck from our mind.
There are interactions from some meds that can make you feel too "controlled". It that case I don't think it is working right. Our thoughts come from our relative state of mind so when you feel better your thoughts become better.