Well the search engines are shown in your FF Profile folder, correct? And FEBE claims to back up the WHOLE Profile, as mentioned by mwang, so that should do it. If you are still suspicious of FEBE then you shouldn't use it, I guess.
You can always go to the Firefox user folder and make a copy of the search engines there. Or make a copy of the entire folder and store it elsewhere, on a CD, an external drive, online data storage, etc.