FC support mutipathing. Each HBA will use its respective path to login into storage. You will configure zoning on A so Fabric A WWPNs can communicate and configure zoning on B so Fabric B WWPNs can communicate. The server will have a boot record to look for Fabric A WWPN value on HBA A. and Fabric B WWPN on HBA B.
For UCS servers, when the HBA bios is loaded, you will see output on the screen for the boot luns that are seen. This will occur for each HBA.
While the the OS is running, both paths are up and available. If one fails, commands will use the surviving path.
Does that help? As a qualified Cisco partner, you may open a case with the PDI Helpdesk to discuss your design strategies.
Thank You,
Dan Laden
Need assistance with an implementation?
http://www.cisco.com/go/pdihelpdesk