init.d scripts boot order

Hello

I'd like to change my init.d scripts boot order. So I changer manually a 
link in /etc/rc3.d with
another ID. But my changes seem to have been "undone" during the boot 
sequence.
So I heard about chkconfig ... I noticed a commented line containing 
chkconfig instructions in
quite every script.
Do I need to manualy change the chkconfig lines in my init scripts ?
Or only apply manual chkconfig 's on the scripts ?
    chkconfig --level 2345 scriptname on (off)

thanks

k.