When you are ready to export your edited video, Kino includes a number of canned scripts for transcoding it into a variety of formats such as flash video. Unfortunately when using the scripts you have little control over the encoding options. If you want more control, you either need to write your own script or better yet modify one of the included scripts.
To get started you can start by reading the Kino User Guide, specifically the Export/Other section. In this section you find out that the scripts are located in $prefix/share/kino/scripts/export/ — $prefix is just a variable name that is specified at compile time. To save you some time for Kubuntu the location of the scripts is /usr/share/kino/scripts/exports.
Copy the script you are interested in modifying and ffmpeg_utils.sh to $HOME/kino/exports/ ($HOME of course is your home directory). You’ll probably have to create both the kino and export directories. Then modify the script to tweak the encoding options — make sure you change the title and profile names so you can tell it from the origianl script, save it, and restart Kino. Your new script should be one of the drop down options for Tools.