I have found the best way to do a real clean setup is to first download the low level format utility from the hard drive manufacturer (maxtor, quantum, etc.) these utilities create a clean hard drive by writing X's to the entire drive, this is desireable because you have no partial file info for the new installation to pick. it is amazing how well windows install can find bits and pieces of an earlier install if you only use fdisk and format.
"Never Argue with an Idiot. They will Lower You to Their Level, Then Beat YOU with Experience"
Easiest way is just to boot from 2k install Cd and use its partitioning tools to remove existing partitions and create new one(s). I would just create partition to install 2k into (ie, if you intend splitting drive into partitions again), and then partition the rest from within 2k using disk management. I say this as you can then make subsequent partitions primary (if you do it during install it will create an extended partition). This is a personal preference - I avoid using extended partitions wherever possible, as they have 'gone missing' on me on a number of occasions.
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