If you are using Logic 8 or prior versions, please create an online support request to acquire the 32-bit file for Native Mode support. Note that you can setup the Faderport in HUI mode using the instructions here.
NOTE: For Logic 64 bit (Logic 9 only), you'll need a special FaderPort.bundle file. See here
1) After you've run the Faderport installer, go to Applications/FaderPort/Logic. You should see a FaderPort.bundle file. Right click (ctrl+click) on it and click Copy
2) Again in your Applications folder, find the Logic application bundle, right click (cntrl+click) on it, and click Show Package Contents
3) Open Contents>MIDI device plugins and paste the new Faderport.bundle file that you copied there, overwriting the previous version if applicable.
Logic should now detect the FaderPort.bundle file and allow you to set up the Faderport in native mode