Nice looking case.
The case is raised so the two bottom 120mm intakes should provide plenty of cooling air.
Do not put it on a rug or you will obstruct the intakes.
If all the intake is from this one source and is filtered, your case will stay cleaner.
Whatever air comes in the bottom will exit somewhere, taking heat with it.
I5-6400 is a 65w processor, it needs minimal cooling. The stock cooler will do the job.
The only reason to use a aftermarket cooler is to get a quieter 120mm fan.
Cryorig H7 would be good.
If the I5-6400 ever gets too hot, it will slow down or shut off.
That temperature is about 100c.
GTX960 will probably try to run at 80c or so to get maximum performance.
The fan will probably rev up to keep it around that temperature.
Graphics cards do run hot but they are built to do so.
One last thing, use no more than a single 120mm fan at the rear to help direct airflow out of your case.
If the exhaust fan is too strong, it will draw in unfiltered air from other openings.