I know this is an old post but just in case anyone still looks in on it...
Your .twmrc will be loaded automatically on login as you say so you can do a lot of your themeing in there but for starting programs automatically it's best to use your .xinitrc
For instance, a snippet from mine goes like this:
/usr/bin/twm &
source ~/.bashrc
feh --bg-scale ~/Dropbox/openbox/images/slackgirl.png &
xclock -digital -strftime "%a %d %b, %H:%M" -render -sharp -face terminal -fg grey80 -bg grey11 -update 60 -geometry 185x30-0+0 &
stalonetray &
dropbox start &
sleep 6
xterm -g 112x47+54+0 -name python -T python &
sleep 3
xterm -g 85x38+150+70 -name Nethack -T Nethack -e nethack &
sleep 3
xterm -g 85x38+150+70 -name CVLC -T CVLC &
sleep 3
xterm -g 85x38+150+70 -name Herrie -T Herrie -e herrie &
sleep 3
xterm -g 92x48+110+30 -name Radio -T Radio &
sleep 3
xterm -g 110x38+150+70 -T Mixer -e alsamixer &
sleep 3
xterm -g 110x46+30+20 -T Lynx -e lynx
http://www.google.co.uk/ &
sleep 3
xterm -g 132x50+15+2 -T ELinks -e elinks
http://www.bbc.co.uk/news/uk/ &
sleep 3
xterm -g 110x46+30+20 -T icq -e finch &
sleep 3
xterm -g 110x46+30+20 -T irc -e irssi &
sleep 3
and so on. It starts twm, loads .bashrc, sets the desktop background, formats the clock and starts a system tray before moving on to starting up a few programs. The programs are all running in xterms and are being sized, positioned and named at the same time. This is only a part of the file but hopefully it gives you the idea, substitute your own requirements obviously.