Since Fluxbox 0.9.15 there has been a new option called session.styleOverlay that allows user to override some or even all elements of style. This comes in very handy for keeping fonts the same for every style or some other things.
Add this line to your ~/.fluxbox/init
session.styleOverlay: ~/.fluxbox/overlay
Then edit the file ~/.fluxbox/overlay like you would edit any style. Add your custom fonts there for example:
menu.title.font: sans-10:boldtoolbar.clock.font: sans-10:boldtoolbar.workspace.font: sans-10:bold*font: sans-8
You could (and should?) also add background options to that file, for your bg to be the one you want everytime you boot.
background: aspectbackground.pixmap: /home/youruser/wallpapers/this_is_a_neat_wallpaper.jpg
aspect can also be centered, tile or random (when you must give a path to the directory, not to a single file)