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MIDI control of audio effect plug-ins in Logic is a bit confusing.
You need to create a new instrument track, and select the plugin as the instrument (it wll be listed under AU MIDI-Controlled Effects->Eventide->Plugin Name). Then, select the track with the audio you want to process in the Sidechain menu in the top right of the plug-in window. Now, if you have the instrument track selected, you should be able to play/record MIDI notes affecting the source audio.