No, FDD drive is using completelly other access methods than other IDE drives. You can simply remove it, but remember to remove it in BIOS, so you won't be worned about fdd damaged or not present during POST.
Much better solution than FDD is buying a Pen Drive. If your mobo support booting with USB devices (ZIP, HDD, FDD) it will also easily boot with such a device. It is easy to manage data stored at USB key, it is just seen by a OS as a HDD. But access times and transfer rate is much higher.
As far as I know CDRinfo is working on a comparison of Pen Drives, so most probably you will see another quality review :)