yes, by adding this line to your prefs.js (or user.js) file:
user_pref("kmeleon.general.searchEngine", "<search url goes here>");
for instance, to search the DICT database, you would use
user_pref("kmeleon.general.searchEngine", "
http://www.dict.org/bin/Dict?Form=Dict2&Database=*&Query="
in the upcoming version, it will be possible to script macros to change this string and call the search box with a single command, so that you could have an entire menus worth of search engines, if you wanted, and choose between them...