Welcome to the forums (and to the world of GNU/Linux). It sounds like you are simply experiencing a common Fedora + fglrx installation issue.
I take it you just double clicked (or ran from terminal) the ATI installer and then installed it from the graphical interface?
Normally all you need to do is simply download the drivers, and then run the installer with --buildpkg Fedora/FC6 and then install the resulting RPMs. However, due to changes in FC6 a few steps must be taken at this point -- though they should get corrected in time for the next release. I have documented the needed changes @ http://www.phoronix.com/redblog/?p=blog&i=NTAwMA
If you follow those instructions, then run the installer with --buildpkg Fedora/FC6, and install all of the RPMs you should be set.