The startup script from fading memory that you put in /etc/rc.d/init.d should take a particular format , take a look at ones that are already there and modify to suit.
Instead of manually creating sym links in each rc.x directory if your script called say, my_server has something like that at the start
#chkconfig: 35 59 34
#description: description of what this is
#processname: my_server
(where 35 are the run levels you want to start, 59 goes the priority to startup and 34 for when shutting down)
You can do chkconfig --add my_server and all the sym links in the right places will be automatically created for you, hopefully