kdm should automatically find that you have installed fluxbox and will display it as a choice.
By this way it is not possible (at least in my Debian 3.1 Sarge with kdm) to use ~/.fluxbox/startup script, but in Debian 4.0 Etch it seems to work.
For Debian 3.1 Sarge, first edit /usr/share/xsessions/fluxbox.desktop:
Comment=Highly configurable and low resource X11 Window manager
changing the bold lines: it's started /usr/bin/startfluxbox script, not just fluxbox. Finally edit ~/.fluxbox/startup:
## uncomment it to launch xscreensaver or idesk
Now it is possible to start a fluxbox session from kdm and use the startup script ~/.fluxbox/startup to fit your needs.