Hi,
Below are few methods which you can choose:
It really depends on which Sup you want to replace ( I mean the one which is currently Active or the Standby sup).
Lets go step by step:
1st-- Think you want to replace the Standby Sup in the working chasis:
Answer: You need not have to worry, just remove the Standby Sup and install the new sup , Make sure the standby sup is running the same software version which Active has.
2nd- Replacing the Active Sup:
Answer: To avoid any distruption, failover to the Standby Sup so that the STandby Sup takes over the active role and then proceed with replacing the Active Sup.
Few reference which might help you:
https://supportforums.cisco.com/discussion/11640021/replace-failed-sup-6500-sup32
http://www.cisco.com/c/en/us/support/docs/switches/catalyst-6500-virtual-switching-system-1440/109334-replace-vss-sup-proc-v1.html
HTH
