Just received my CLC 240, my first foray into water cooling.  I just want to be sure whether the cables from both fans are to be connected to the "to fans" connectors from the pump module.  My MB (ASUS Maximus X Hero) has connections for AIO Pump, as well as 2 CPU fans.  Would it be better to connect the two fans directly to the MB to control them or use the fan cable from the pump module and have the pump control everything?  Also, if my MB can control everything, do I need to connect the USB cable also?  I wonder if the Flow Control will cause conflict.

USB connection is so you can control the fan/pump speeds through the software. If you don't plug in the USB cable it will run as the default fan/pump profile.