Casey,
If you have any question re *nix systems let me know
Been a *nix sysadmin for many many years; Always glad to help out
Contact me direct if you want to prefer this offline :)
General rule of thumb though is add a (ba)sh script into /etc/init.d/
then Symlink a name from /etc/rc3.d/S99mystuff -> /etc/init.d/mystuff
I normally just copy an existing script in init.d & hack in what I need
or cheap 'n cheesy just add the commands to the end of /etc/rc.local
If the programs don't fork themselves into the background add a " &" at the end of the command line to force it to. (don't type the "'s)