Updating the PS or PZ is actually quite straight forward. You just need ssh access and then execute a short list of commands (mind to call screen so that things are communicated):

ssh <server>
screen -x
cd <dir> 
./update -w
cp -Rf bundle/* autopilot

where <dir> = [ svn-public | svn-prozone ] and <server> the server's IP

Now change to the autopilot tab and close the server:

save
exit

Restart the server: . /autopilot.tcl load | tee -a logs/<psgnr> where <psgnr> is the number of the currently running or to-be-started game.