Ok I'm going to be painful detailed on this to try to find the right answer to my problems.
I have Adobe CS 5.5 I upgrading After Effects separately before I bought the rest of the suite, I use to be a final cut pro owner. Instead of downloading all of my plug ins again. I made a Alias folder to transfer all of my plugins from Red Giant. Everything was good, then I upgraded to the suite and re downloaded the plugins for adobe premiere pro.
Now here is the problem. When I open After Effects, it says that there are duplicates of my red giant plugins. I go through the MacHD>App Support>Adobe>Common>Plug-ins>CS5.5>Mediacore and bam! I do see the duplicates and drag them to my Alias folder. My Warning message are gone but so are my plugins in Adobe Premiere. It's a endless cycle of trying to find a way to keep my Plugins in Premiere without having that annoyed message come up every time I start After Effects. Is there a way I can turn it off, or just move my files so they can be seen in Adobe Premiere too.
It sounds like you're going about this backwards. You said something about moving files to an alias folder. You don't need to move anything if you're using an alias. The purpose of an alias is just to point to the existing location.
Don't move the plug-ins from your MediaCore folder. If you need an application to see the plug-ins in your MediaCore folder, then add an alias in the plug-ins directory for that applciation, and make that alias point to the MediaCore folder.
See these pages:
Here are instructions from Red Giant:
If you're having trouble installing Red Giant plug-ins, contact Red Giant support.