I am extremely new to After Effects. I am looking to download and try the CS4 version. I was wondering if there was an export option to FLV video, and place into some sort of XML menu template. Possibly, preserve markers translate them as chapters into some sort of User Interface template... am I far off on this? Is this possible through After Effects and/or Adobe Encoder?
You can export FLV files with cue points based on markers. See "Web links, chapter links, cue points, and markers".
More information on rendering and exporting to FLV is in "Render and export a composition as an FLV or F4V file".