Pal2EA lets you place all your character palettes in one text file then generates EA installers for you. It handles the insertion as well as setting the palettes to characters or animations. Check the read me for examples of how to set up the palette text file.
Updated to v2.1 to fix a problem with FE7/FE6 compatibility
When switching to a new version delete
palette definitions.txt so that pal2ea can generate the updated definitions file