I think what you may be missing is on pg 20, 'Creating a Store', which starts like this
Creating a store
Before creating a store, make sure the root directory of the stores has been configured and the physical storage disks (LUN devices) are formatted and mounted on the StoreOnce Software deduplication system. The LUN devices may be on local disks or a disk array (SCSI or Fiber Channel interface) or on a NAS device in the same LAN (iSCSI interface). When using iSCSI interface, the reliable network connection must provide a latency of at most 2 ms and a throughput of at least 1 Gbit/s.
A store can be created from:
The GUI: Follow the procedure for adding a device and when prompted, specify the name of the store (see below for details).
The CLI: Use the command
StoreOnceSoftware --create_store (see Appendix A: StoreOnceSoftware utility for details).