You put links in the rc<n>.d directories to start and stop the process
at the specified runlevels, where <n> is a given runlevel.

Here are some links to scripts to start Folding at Home (whichm unlike
some here, i've never had any trouble with):

jbuchana@zaphod$ find . 2>/dev/null| grep folding
./rc6.d/K06folding
./rc0.d/K06folding
./init.d/folding
./rc2.d/S99folding
jbuchana@zaphod$

The "find ." command lists all the files in or below the current
directory, the "2>/dev/null" redirects any error messages to nowhere,
and the "grep folding" filters out the name "folding", listing the
links in the rc<n>.d directories.

Here's a long listing of one of them, the one that starts it up:

jbuchana@zaphod$ ls -l rc2.d/S99folding
lrwxrwxrwx 1 root root 19 2008-11-13 21:20 rc2.d/S99folding ->
/etc/init.d/folding
jbuchana@zaphod$

I made the links with the "ln -s" command, "ln -s /etc/init.d/folding
/etc/rc2.d/folding".

The links that start with "K" kill the script on shutdown.

I hope that wasn't too terse, I've had a rough day...