From the FluxBox FAQ:
# window manager
fluxbox & wmpid=$!
wmnet -x 70000 -d 300000 -L cablemodem -w &
# HANG POINT - wait for windowmanager to exit
That is the suggested context of your .xinitrc file. The bbrun, wmCalClock, wmnet, and wmxmms are all apps that will start when fluxbox starts so add whatever you would like in there.