In order to install/upgrade ConfigMgr the following commands and steps must be used, not rocket science but not documented anywhere either;

1. Uninstall WAIK 1.0
   • MSIEXEC.EXE /x {31E8F586-4EF7-4500-844D-BA8756474FF1} /qn REBOOT=REALLYSUPPRESS
2. Reboot Server (Yes, it's a must!)
3. Run ConfigMgr SP1 PrereqCheck
   • SETUP.EXE /PREREQ /NOUSERINPUT
4. Install ConfigMgr SP1
   • SETUP.EXE /UPGRADE <FULL_PATH_TO_PREREQ_PATCHES_WITHOUTSPACES>
5. Install ConfigMgr R2
   • MSIEXEC.EXE /I ConfigMgr2007R2.msi /qn

If you are building from scratch, its easier to use the slipstreamed SP1 media! :D

As always, when copying code ensure that quotes and dashes are correct before running commands, " and " are not the same!

Have fun!