You should be able to telnet to the switches and configure zoning. I'm assuming you're using WWN Zoning - not much different for Port Zoning.
Brocade, Logon as admin
>ZoneCreate "ZONENAME", "WWN", "WWN".... Create new Zone
>cfgAdd "CFG_NAME", "ZONE_NAME" Add new zone to config
>cfgSave Save the new config
>cfgEnable "CFG_NAME"Enable the new config
McData - logon as Administrator
>config zoning -- gets you into the correct directory
>replaceZoneSet -- copies the Active ZoneSet into the Working area
>addZone <ZONE_NAME>
>addWwnMem <ZONE_NAME> <WWN> -- add each WWN required in the zone
>activeZoneSet -- Overwrites Active ZoneSet with the working ZoneSet
For both the above, consult the user guide first, but that should be in and around what you're looking for.
J