Lately after a use of 6 months of my AMD FX8350 CPU I'm experiencing high temperatures and loud noise coming from the CPU fan(I set that in order to keep it cooler).
I decided to replace the stock fan with a water cooling system in order to keep my CPU quite and cool and add one or two more case fans too.
Here is my case's airflow diagram: http://www.coolermaster.com/microsite/silencio_650/Airflow.html
My configuration now is:

• 2x120mm intake front(stock with case)
• 1x120mm exhaust rear(stock with case)
• 1 CPU stock

I'm planning to buy Corsair Hydro Series H100i(www.corsair.com/en-us/hydro-series-h100i-extreme-performance-liquid-cpu-cooler) and place the radiator in the front of my case(intake) and add an 120mm bottom intake and/or an 140mm top exhaust fan.

My CPU lies near the top of the MO.
Is it a good practice to have a water-cooling system that takes air in?
As you can see here the front of the case is made of aluminum. Can the fresh air go in?
Does it even fit?

If not, is it wiser to get Corsair Hydro Series H80i (www.corsair.com/en-us/hydro-series-h80i-high-performance-liquid-cpu-cooler) and place the radiator on top of my case(exhaust) and keep the front 2x120mm stock and add one more as intake on bottom.

If you have any other idea let me know.
Thank you.

EDIT: The CPU fan running ~3000rpm and temp is around 40~43C on idle and save energy.
When temp is going over 55C when running multiple programs and servers on localhost(tomcat, wamp) rpm is around 5500 and loud!
I'm running Win8.1
CPU not overclocked

PS: Due to my reputation i couldn't post the links that was necessary. I will edit ASAP.