I assume CCC does essentially the same as SD, but as long as it makes a bootable dupe, then after a clean install, you can use Migration Assistant to pull EVERYTHING from the previous install over (apps, docs, settings, iTunes, iPhoto, etc.). With SD at least, you can select "From another Mac" or "From Another Volume on this Mac"--both are functionally equivalent at this point.
The "cleanup" is when you move apps from the Apple default location (Applications folder) into user-defined subdirectories for whatever reason (I don't like 300 apps in one directory--I subdivide into "Comm-Web", "Media", etc.). Leopard will assume most of them to be at the root of the Applications directory, so after migration, it'll show a bunch of "?" in the dock for those moved apps.
Just trash the "?"'s, open the migrated apps that you had in the Dock before the upgrade, and while open, right-click and select "Keep in Dock" and you're back to your pre-upgrade state. I end up changing a bunch of stuff anyway after an upgrade, so it's really not a big deal.