You may already know this but if this helps good! Easy way is if it is a common app: (I looked for it in synaptic but could not find it). First go to a terminal and type: update-menus. This will do exactly that. Then go to .fluxbox in your home folder (click on view to change from hidden to unhidden folders) open up the file called Fluxbox-menu. At the top of the file there are directions on how to make your own menu to use. Once that is done, you can copy and paste from the Fluxbox-menu, to your own. From there you can also see how to make links to open apps that dont appear in the flux-box menu when you "update-menus" Also, you can get rid of a bunch of crap you dont need to see in your menus by just deleting it. "update-menus" will update the fluxbox-menu but not your own, so . . . . you have complete control over your menus.
If this isn't what you need let me know and we'll go to the more complicated way. Also look at http://fluxbox.sourceforge.net/docbook/en/html/
for more info.