Generally, if you already have a Sup-II as your controller in Slot 1 in the 6509, you should just be able to insert the new card into Slot 2.
When you insert the card, the 6509 will detect it, and will copy the configuration from the active Supervisor to the redundant Supervisor.
The problem you may have with this is that different IOS/CatOS versions have different commands (or the same commands, but the syntax has changed) so some of your configuration may not copy across successfully. It is therefore beneficial to ensure that both Supervisor cards are running the same version of CatOS/IOS.
When we replaced a failed Supervisor-II card last year, we scheduled some down-time to do this. We took down the switch completely, and disconnected all the connections, save for Power and Console. We removed the active Supervisor (which had a newer IOS revision than the new redundant card), and inserted the redundant card. We upgraded its CatOS version and the IOS version running on its MSFC to match those on the existing, working card. We then powered down the switch again, removed the new card, put the old card back in, and booted.
Once the switch was back up and running on the existing card only, we put the new card in. The active card copied the config to the new backup card, and we reconnected all the network cabling and fibres to the switch to bring the network up again.
I hope this helps!