I have two Cat 6500 running as active/passive. Both have 48 port modules. Now if I need to define a trunk between both the Cat 6500 i.e. for switch traffic, will it have to be defined on the ethernet module or would the link between both the Supervisory engines (Gigabit Ethernet ports) will do the job.
You can use either or both. Generally you want a group of ports ie. an etherchannel for throughput and then you configure the etherchannel as a trunk.
As long as the speed/duplex settings are same you can mix fibre and copper into the same etherchannel.