You probably won't have to recompile your kernel. Only the loadable kernel module from ATI needs to be recompiled, and that's through the two scripts mentioned in previous posts.
You won't see the agpgart kernel module if you're booting into init 3. If you want to see if you're properly loading the kernel modules, try firing up X through startx. Then switch to another console using CTRL-ALT-F2 or one of the first function keys (at the top of the keyboard).
Now when you run lsmod you should see both the agpgart and fglrx modules loaded.
Heck, why not run fglrxinfo while you're at it, and see the ATI driver running.
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