Unfortunately, the mobo manual does not answer this question, but hints that the answer is "no".
In the manual Section 3.7 Monitor (in BIOS Setup), on p. 3-40 it says that the CPU Q-Fan Control settings include "Advance Mode" which makes the CPU _Fan port behave as a 3-pin fan port. But on the next page where the three CHA_FAN port settings are detailed, there is no such setting. It says that "Enabled" will turn on the Chassis Q-Fan Control, and implies that it is only able to function as a 4-pin fan port. If you connect a 3-pin fan to a 4-pin port, the fan will always run at full speed because it cannot use the PWM signal from the 4th pin.
In Chapter 4, page 4-11, it tells you how the Fan Expert 2 (software on the support CD) works, but does not address your specific question. Moreover, it is vague by saying that the details of the software you get depends on the mobo you buy, and on what they decide to change as time goes on.
Bottom line is, if you really want to use the mobo's automatic control feature for the chassis fans, you most certainly CAN do that IF you buy 4-pin fans. BUT since you are buying 3-pin ones, the manual suggests it won't work. You most certainly can try it that way, and it just might work even though the manual does not say that clearly. If it does not work, there's no harm done. You will get more cooling that you need (all fans at full speed), but no automatic control. Then you can move the fan connectors to the case's manual control system and use that.