You should be able to configure NetFlow via a FlexConfig, as long as your ASA software version supports it. Double check the configuration guide to see all of the commands you'll need to configure (you need to enable it in a service policy as well):
Here is also a guide we have written on exactly what commands will be needed http://supportforums.cisco.com/docs/DOC-6113 If you have CSM earlier than 4.0 you can just put the commands in the Flex Config in CSM as mirober said and then just delploy it to the device.
We have configured the outside and inside Interface with official ipv6 adresses, set a default route on outside Interface to our router, we also have definied a rule , which also gets hits, to permit tcp from inside Interface to any6.
In Syslog I also se...