Just throwing in my two-cents-worth here. I've used ASUS and Intel motherboards.
It seems fairly clear from the user's manual and specs as to how many amps can be powered by the combination of motherboard fan headers (a total 12V amperage), or conversely, the average amperage of fans distributed across those headers. If you only power one fan from the motherboard and use the remaining fan-headers exclusively for monitoring (providing the power via molex plugs from the PSU), you should be safe if you stay within the TOTAL amperage spec for the motherboard's fan headers.
There are several front-panel controllers available now which connect to the computer via USB, allowing for software speed settings and temperature control or variation for those settings.
But barring the desire to add the extra equipment, my choice is to run my CPU fan off the appropriate fan header and the remaining case fans from a manually controlled front-panel controller. My mobo provides a total fan-header power of 12V x 1.8A. I'm running a 0.8A (12V) Delta fan off the mobo CPU_FAN header, and only monitor wires are connected to the remaining headers. There has only been a slight increase in temperature measured from the mobo temp sensor -- maybe 1C increase.
At least with this configuration, I can load up Alfredo Comparetti's "SpeedFan" among my "startups" -- varying the speed of my Delta 120mm between about 2,600rpm and 3,400 rpm. The fan's top-end is 3,700, with 142 CFM air-movement, but anything over 119CFM doesn't increase the effectiveness of my ThermalRight XP-120. That also means that I'm effectively drawing less than 0.8A of current from the mobo.