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
(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