For details on using ffmpeg2theora, you can double click on the ffmpeg2theora icon. You should see a list of options such as:

ffmpeg2theora 0.16

  Usage: ffmpeg2theora [options] input

General output options:
  -o, --output           alternative output filename
  -s, --starttime        start encoding at this time (in sec.)
  -e, --endtime          end encoding at this time (in sec.)
  -p, --v2v-preset       encode file with v2v preset.
                          Right now there is preview and pro. Run
                          'ffmpeg2theora -p info' for more informations

Video output options:
  -v, --videoquality     [0 to 10] encoding quality for video
                          (default: 5)
  -V, --videobitrate     [1 to 16000] encoding bitrate for video (kb/s)
      --optimize         optimize video output filesize (slower)
  -x, --width            scale to given width (in pixels)
  -y, --height           scale to given height (in pixels)
      --aspect           define frame aspect ratio: i.e. 4:3 or 16:9
      --croptop, --cropbottom, --cropleft, --cropright
                         crop input by given pixels before resizing
  -S, --sharpness        [0 to 2] sharpness of images (default: 2).
                          Note: lower values make the video sharper.
  -K, --keyint           [8 to 65536] keyframe interval (default: 64)

Audio output options:
  -a, --audioquality     [-2 to 10] encoding quality for audio
                          (default: 1)
  -A, --audiobitrate     [32 to 500] encoding bitrate for audio (kb/s)
  -c, --channels         set number of output channels
  -H, --samplerate       set output samplerate (in Hz)
      --nosound          disable the sound from input

Input options:
      --deinterlace      force deinterlace, otherwise only material
                          marked as interlaced will be deinterlaced
  -f, --format           specify input format
      --inputfps fps     override input fps
      --audiostream id   by default the last audio stream is selected,
                          use this to select another audio stream
      --sync             use A/V sync from input container.
                          Since this does not work with all input format
                          you have to manualy enable it if you have
                          issues with A/V sync

Metadata options:
      --artist           Name of artist (director)
      --title            Title
      --date             Date
      --location         Location
      --organization     Name of organization (studio)
      --copyright        Copyright
      --license          License