I really know nothing when it comes to customising a fluxbox desktop,
in /home/yourname/.fluxbox there is an init file that you can modify to change things like the background, for instance if you have a picture you want to set as background on fluxbox, you would edit the line :
and add "fbsetbg -f path to your picture, such as /home/jay/jay.jpg
so it would read:
session.screen0.rootCommand: fbsetbg -f /home/jay/jay.jpg
and when you restart fluxbox, the image should come up as your background.
you can get more info about this in the man page for fluxbox..
as for your running applications, look at it like this. if you run kde and start for example the galeon webbrowser, which is part of gnome, you're only starting galeon, not gnome. same thing when you run applications in fluxbox. you're only starting the application, not the entire desktop environment.
it's pretty easy, once you've done it once or twice lol...