Hello,
You can create layer 2 port-channel and make it a trunk port. Then you can create SVI's for the vlans that you want to be part of Layer 3. Add those vlans to be allowed on the trunk or you can leave the trunk port as is to allow all the vlans.
This way you can have both layer 2 and layer 3 traffic pass through the etherchannel. Sample config of port-channel below.
SW5(config)#int rang e0/1-2
SW5(config-if-range)#chann
SW5(config-if-range)#channel-gr
SW5(config-if-range)#channel-group 1 mode on
Creating a port-channel interface Port-channel 1
SW5(config-if-range)#int port-channel 1
SW5(config-if)#switchport
SW5(config-if)#switchport trunk encap dot
SW5(config-if)#sw mode trunk
SW5(config-if)#exi
SW5(config)#vlan 100
SW5(config-vlan)#exi
SW5(config)#interface vlan 100
SW5(config-if)#ip add 100.1.1.1 255.255.255.0
SW5(config-if)#no shut
SW5(config-if)#
Hope this Helps.
Please let me know if you have any further questions.
Regards
Vinit
Thanks
--Vinit