Sango,
For Emulex and Qloigc HBA's you will need to break into their respecitve OptionROMs during POST. From the Option ROM you can make changes to the HBA behavior. There are no Cisco utilities to perform this, i.e. nothing in CIMC for Qlogic or Emulex.
But, in general, if the HBA is working and no changes have been made to the default firmware configurations, it should flogi into a SAN switch without configuration
Would you list the vendor and model number and what you are trying to do? What is the SAN switch model you are connection to? Data access only, SAN boot?
Thanks,
Dave