Controlling CPU fans with a fan controller

Pondering controlling my CPU fans with a fan controller on my new air cooled build. Is it more beneficial to let the motherboard control the fans or set the fan rpm's myself with a fan controller.

I'll be using 2 Zalman 9500's and an AquaComputer Aquaero. The Zalmans come with an inline fan controller but will not be using those ugly apparatus.

Define "more beneficial"....

Less noise? Lower temps? Complete control?

Generally speaking, a motherboard will lean towards being quiet vs. keeping cool - unless you can set the temps yourself, in which case, get Ron Popeil on it.

usually the bios take care of this these days