Try this :
to get fan speed for card 0
export DISPLAY=:0.0; aticonfig --pplib-cmd "get fanspeed 0"
to get fan speed for card 1
export DISPLAY=:0.1; aticonfig --pplib-cmd "get fanspeed 0"
to set fan speed for card 0 to 50%
export DISPLAY=:0.0; aticonfig --pplib-cmd "set fanspeed 0 50"
aticonfig claims that I changed the fan speed, but it is still the same loudness. And I don't believe any other fans are to blame. Also, the old fan speed appears again after a restart.