OS X V10.7 Lion :: Free Space Fragmentation?

I recently downloaded the iDefrag demo and it reports that my files are 0.7% fragmented but the free space on my disk is 75% fragmented, what does this mean?  Should I be concerned and should I defrag the drive?  My mac seems to take forever to boot up these days and programs open very slowly.  I work with quite large Photoshop files regularly, but my scratch disk is set to a different drive to the system disk. 

Any recommendations for the best way to learn about troubleshooting the Mac would be appreciated, as I'm keen to avoid any down time due to failures of any kind (I don't mind investing some money for the right training).  The area I'm particularly interested in is restoring a system, if there are certain corrupt files, but doing this without affecting all the third party program files etc.  I use carbon copy cloner to keep an exact copy of my system disk but am worried that if the system files becomes corrupt, I'm just making a copy of the corruption onto another disk!