fluxconf was a tool to configure fluxbox's init file, edit the menu and the keys file. It is now so old that it will break your init file, menu, and keys file. Most modern distributions have removed this tool from their repositories.
A nifty alternative to the menu configurator is Zan's fluxMenu application (last updated 2007, current state unknown).
Most of the options that are set in the init file are configured via the config part of the rootmenu.