As soon as you call the amd-installer without buildpkg option it directly writes files at places which will NOT be the position you get with the fglrx ubuntu package. jockey is the name of ubuntu's the restricted modules manager and allows the install of binary drivers from the ubunut repository. When you mix that your system will most likely break on the next update. As U has got latest 8.96 drivers for 12.4 i would not use the amd-installer at all for this version. My script basically checks for the Ubuntu version, then it installs the needed depends (maybe a few more which have been needed for older releases, some will fail on newer distributions but those are not critical) then it applies patches to the fglrx module for better kernel support if needed. In case of Ubuntu it just creates the packages using buildpkg option, deletes all older fglrx packages, installs the new ones, calls aticonfig to write a /etc/X11/xorg.conf file. This step is not done by ubuntu normally as they install one additional package which i just delete as it is not required (and useless) on Debian. The script therefore works on Debian up to Squeeze, it does not (yet) work for Wheezy/Sid. There i patch some things to use Ubuntu packages on Debian. With current drivers i would not need to patch that much (just a few depend issues), informer i needed to override the XORG driver version depending on the installed X because up to 3 different variants have been shipped in the amd installer - this is now unified.
This was the general way what my script does, but what is also different is what happens when it detects radeon kms drivers nor not. Compared to nouveau kms which can be unloaded with a trick and then you can switch over to nvidia binary (using screen) this is not possible for fglrx. It worked with radeon without kms, but not always. It works more often when (older) fglrx is running, but not in all cases. You need to stop X in that case then you unload fglrx and install everything then you start X up again. This way you can avoid a reboot. If you want to make it saver you can FORCE the script not to stop X at all even when it would be possible in theory. The "-z" option is just for this and is default when radeon kms is detected. In that case you have to reboot to activate fglrx.
But: i only test Ubuntu when a new release is in first alpha or directly after release. Usually it should work in the development time between as well, but i have got no permanent U install.