If you already have, put your scripts in /etc/rc.d/init.d. There's a standard set of parameters the scripts should take, e.g. "xyzscript start", "xyzscript stop".
Now, you need to make sure they're going to run. There are some predefined directories in /etc/rc.d called rc.0, rc.1, etc. "man init" for a full description. You will probably want to add your script to rc.local. So, do this.
ln -s /etc/rc.d/init.d/xyzscript /etc/rc.d/rc.local/99xyzscript
Now, the next time you reboot, your script will be automatically called with "xyzscript start", and when you shut down, it will be called with "xyzscript stop".
The scripts will be executed as root. you can su to another user when you execute a program inside the script.