140mm fans more air at a given rpm than 120mm.
I would opt for 140mm front intakes where possible.
Use the 120mm rear more as a guide to direct the heated air out of the case.
Whatever comes in the front will exit somewhere, taking heat with it.
Connecting a fan to the motherboard will allow dynamic fan speed control.
I find that annoying.
I like to use fan speed reducing cables and run them at a constant speed.
With two front 140mm intakes, you will get all the cooling you need for a good air cpu cooler and a hot graphics card.
In addition, if all the front intake air is filtered, your parts will stay cleaner.
Don't screw things up by adding more fans.
They will tend to draw in unfiltered air.