Cisco controllers that support channeling actually use a simplified version of channeling referred to as "LAG", Link Aggregation.
Lag requires that the switch connected to the other end of the channel be configured for source/destination ip (src-dst-ip) etherchannel load balancing:
http://www.cisco.com/en/US/docs/wireless/controller/7.0/configuration/guide/c70mint.html
"The recommended load-balancing method for Catalyst switches is src-dest-ip (CLI command: port-channel load-balance src_dest_ip)."
With 6500's running in pfc3 mode, the channel load balance method is 'src-dst-ip enhanced' or 'src-dst-ip vlan included' by default, which will often cause packet forwarding problems with Wism controllers (referenced in the link above).
6500's pfc mode can be verified with this command:
6500#show platform hardware pfc mode
PFC operating mode : PFC3A
The ability to revert to 'src-dst-ip' only was not originally in 6500 code.
This was added as an enhancement in 12.2(33)SXI3 as documented in the following enhancement bug:
http://tools.cisco.com/Support/BugToolKit/search/getBugDetails.do?method=fetchBugDetails&bugId=CSCso79925
Once running this code, the correct port channel load balancing can be enabled with the following configuration:
Config t
port-channel load- balance src-dst-ip exclude vlan
6500 VSS pairs will most likely be operating in pfc3 mode, as pfc3's are required for VSS support.
Assuming that the channel load balancing algorithm is correct, WLC's should be able to form Lag etherchannels with ports connected to both VSS physical switches, as the VSS is one 'logical' switch.