|The side fan "may" disrupt airflow thru the case, it "may" blow cool air directly on a temp sensor and give a reading that is lower than the actual temperature a component is operating at, or it "may" actually be beneficial; only testing would tell the truth.|
I don't understand your last question. If you have any filters in place, leave 'em in place. Other than that, cool air will enter at the lower front area (call it point A) and exhaust at the upper rear (call that point B)area. As the air travels from A to B, it absorbs heat from the various components (hdd's, motherboard, video card) and spits that heat out into the room.
So, looking at the pic, the cool blue air turns into warm red air The actual temperature rise is (or, a few years ago, was) something like 5-6°C.
This is all generalized and you can find the best configuration, temps, and noise level if you want to invest quite a bit of time to see what works best for you.