Try this:
Send your sequence over to Soundtrack Pro: Send to STP Multitrack Project. Your markers will be visible. Now show the Podcast Track. It will appear below the Video Track. Duplicate the location of your video markers over to the Podcast track using the Blade Tool, or Shift+Command+M at the location of the playhead.
Now from the STP Menu: Export – FileType to Podcast/AAC file. Press the Podcast tab and select the Enhanced (images) option. This will output an audio only AAC file with a video still from the start of each selection (chapter). You can customize what chapter data is displayed in the STP Details tab prior to exporting. Just make sure you have the Podcast track selected prior to editing.
As far as searching for markers in FCP, have you tried right clicking a marker? The pull down menu will display each marker for easy access.
-paul.