I also have the Antec 900 case. I couldn't figure out how to get the fans connected to the mobo... so i didn't. They have a molex connecter for power to the fans, but then the fans all have a manual switch for speed. The switch has a setting for L (low) M (medium) and H (high) and the default setting on mine were all LOW.
Ive been running my comp q6600 OC to 3.0 GHz with a asus HD 4850 gpu stock OC to 680/1100(if i remember correctly) and the temps all seem very good. So maybe the low setting is good on the case if your not going crazy with gpus.
If someone knows how to get the fans connected to the mobo i'd be interested in knowing how. Im sort of a noob
Edit: Bingy after re-reading your post it sounds like your talking about trying to connect the 4-pin floppy drive power connector on the end of your daisy chain of fan power connections to the cpu_fan slots on the mobo. I don't think it will fit and/or work... Sorry hard to explain, but if your asking what im thinking you'll understand.