Unfortunately, with ACS 5.5 you cannot generate a CSR with SAN or DNS of different ACS FQDN's in your network.This feature has been introduced in ISE. However ACS does except the SAN certificate w/ private key file.
SAN certificate with ISE
http://www.cisco.com/c/en/us/td/docs/security/ise/1-2/user_guide/ise_user_guide/ise_man_cert.html#pgfId-1171325
Regards,
Jatin Katyal
~Jatin