According to the source code, it uses GConf to store configuration. Gconf can be manipulated from the command line using gconftool-2 but you do need to understand the schema because gconftool is pretty low-level and can't ensure that your changes are correct or consistent.

You might find it easier to use the nautilus action configuration tool to change an action and gconftool to see what gets changed than to make sense of the schema description directly.