Hi,
You wrote " With SUP1A running cross module etherchannel, would the behavior same as normal etherchannel group? ", yes it will be a normal ether-channel group.
"Someone told me that the traffic will only go through one of the ports in a group. e.g. Port 1/1 of Group 1 will transfer packet but not port 2/1 and Port 2/1 of Group 2 will transfer packet but not port 2/2. Is that true?.............. Nope that's not true. Ports ports on the Sup engine are active and will forward the traffic.
If you remove the active Sup, the traffic forwarding depends on the kinda of redundency we have configured. For example if you High availability configured on the sup it takes around 5 -10 second before the second sup takes over the resposilbility of traffic forwarding on layer 2. For L3 you configure MSFC for SRM and DRM to take care of the traffic routing.
Configruing Ether-channel :
http://www.cisco.com/univercd/cc/td/doc/product/lan/cat6000/sw_7_6/confg_gd/channel.htm
Configuring Redundency :
http://www.cisco.com/univercd/cc/td/doc/product/lan/cat6000/sw_7_6/confg_gd/redund.htm
HTH,
-amit singh