"jailbait...why is this not good to do? I recall someone telling me that apt is perfect for these types of upgrades...can problems arise just from using apt or are the issues related to the differences between RH 9.0 and FC1 or FC2?"
There are several possible problems. apt occasionally stumbles over complex updates. If apt makes a mistake then portions of your new system will be unusable.
It is very common for any new install to have problems. If you are dual booting then you are under no time pressure to fix the problems. If you have destroyed your old system then you have to get the problems fixed immediately in order to have a working system.
Be prepared. Create a LifeBoat CD.