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If I understand you correctly, you installed AA independently of 25Assist.

In that case Assist probably wont recognize your version of AA as the right one and you wouldn't be able to play until you let Assist install AA for itself.

Before I installed AA independently it would still seg fault immediately after launch not letting me do anything. Can I just tweak a config file to use the new auth server?

No, you have to run though Assist.

Make sure you have 32bit compatibility libraries installed.You should have both a /lib and a /lib64 folder in root.  Assist is 32 bit, as well as AA.  If you don't have 32bit libs, you might have to install them.  I'm not familiar with fedora 18, but it'll be something like "yum install glibc.i686".  Google it.   You might also have to install libstdc++ separately.  Use ldd on the AA executable to figure out what you need.  If ldd output shows something not linked to a memory address or file (or symlink) it could explain a lot.  Sometimes, after installing a 32bit library compatibility package, it may not have created all the necessary symbolic links to the library file needed by AA and you'll have to create them.
I have never run the linux client before, so the only other thing I can think of is maybe research graphics compatibility, maybe the linux AA client needs opengl compatibility?    ia32-libs-gtk might be needed as well.
Check the log files for clues also.