BS2000 consists of a "Basic Configuration" plus optional, chargeable products; each of this optional products may add some more commands to the JCL. Therefore you won't find any general "JCL" manual.
To get started, try the manual server
http://manuals.fujitsu-siemens.com/serv ... man_us.htm and select the BS2000 version you have. The "Command" manuals cover the BS2000 basic configuration.
Among the optional products, SDF-P should be of most interest, because it adds high-level JCL commands (execute loops etc.) The manual as well gives some hints about procedure programming with SDF-P.
Good luck!