It's not necessary to uninstall the CF application profiles. The files are overwritten with a new install, so the old version is no longer present. The only side effect of doing this is having a worthless uninstall entry in the registry.
While the driver install does not prompt you to reboot, you should. Crossfire is disabled until the driver is reloaded. The simplest way to do that is rebooting. You can also reload the drivers by disabling the graphics card devices using DEVCON, then re-enabling them (with a batch file, since the screen goes away once you disable). The application-specific 3D settings also go away until a reboot, and I have not yet found a way to restore them otherwise.
So, the short answer to the OP is, reboot your computer after installing new drivers.