I have an intel server board S5500BC with latest firmware, its running normally and quite ! my problem is that my HDDs are getting hotter about 45C - 50C which isnt normal according to acronics free HD monitor tool, now is there a way i can speed up the fan behind the HDDs and the rear fan so i can drive more air inside and therefore hot air out?
Not manually, no. The temperature sensors for inlet are on the front panel, so they are probably not detecting the overheating on the hard drives.
Which chassis are you using? Is it a pedestal with an 92mm fan behind the hard drive cage?