In each n-runlevel (rcn.d), some "services" (which actually are scripts who execute services or commands) are started and some are killed. Some distributions, like Debian, actually "jumps" some runlevels (if I'm not wrong, from 3 to 5) because it's more quick to start the system that way.
In /etc/rcn.d/ you will find some symbolic links to scripts in /etc/init.d. Those links are named S** or K**. That means that they are being Started or Killed in that runlevel. The two following numbers are telling init in which order they are being started (or killed). Sometimes, a script which is runned first is going to be killed last (in some way, scripts might need 'dependencies' and that's what the order says).
It's ok to have two Sxx or Kxx with the same numbers (when one adds a script which doesn't need others to be runned, one probably will link it as S99 or K99 -start and kill at last-).