YES!!! run both defrag AND scandisk first.
we had a person in here a week or two ago who was having MASSIVE problems because they failed to run defrag first.
when you install linux to dual-boot with win9x or ME, then the hard disk needs to be partitioned up in two - if you don't run defrag, then any windows data or programs that are on the second half of the hard disk will be destroyed. even if you aren't using that much of your hard drive, there might still be some files on the extended parts of your drive. defrag will move anything that's there onto the first half of the drive, and leave the second half free for linux.