Hello Join,
I suppose you are doing a port-channel of G0/1 and G0/2.
int gi0/1
switchport
switchport trunk encapsulation dot1q
switchport mode trunk
channel-group 1 mode on
!
int gi0/2
switchport
switchport trunk encapsulation dot1q
switchport mode trunk
channel-group 1 mode on
!
interface Port-channel1
switchport
switchport trunk encapsulation dot1q
switchport mode trunk
do this on both switches
for making first c3550 root bridge for all vlans
spanning-tree root primary
on second
spanning-tree root secondary
Hope to help
Giuseppe