BES is started at system boot time by the S99POWERpack script. Depending on your OS, the S99POWERpack script will be under one of the /etc/rcX.d/ directories, for example:
There is also a K99POWERpack script, which shuts down BES (kills) on system shutdown.
Usually, on a SysV based system, there is one version of the startup/shutdown script (POWERpack) and the S99* and K99* scripts symlink to it (POWERpack script usually stored under /etc/rc.d/init.d - may vary depending on your OS). So in essence, there is no real difference between the S99* and K99* scripts - they both point to the POWERpack script which runs at server startup (S) and shutdown (K).
And just in case you were wondering, the number (99) stands for the boot priority e.g. S10 would start before S99.