If I understand your inquiry correctly, then yes... all you really need for a fresh start is the cd from your manufacturer (presumably a copy of Windows XP)
if you're nuking everything (full format... not "quick format") then yeah, sometimes it will take as long as 108 minutes to wipe your drive clean. From there, you will be installing a fresh version of Windows XP. Hopefully you backed up everything you needed and you have copies of all the software and drivers you will need afterwards...
As far as determining where to boot from.... that is handled in your bios.... at the very beginning of a boot when your computer tells you to presss "Del" to run setup.... yeah, it's in there, under boot. Normally, you'd want to order it so that it checks cds first (before the hardrives).
The long waits are normal, though, so don't worry about that. A fresh install is usually a day's work.
Hope that helped some.