londint,
You have to create the Layer 2 vlans in the Catalysts, and then configure one Switched Virtual Interface (SVI) for each layer 2 vlan. For example, if you have VLan 2 on SWITCH 1, and VLAN 3 on SWITCH2, and you want inter-VLAN routing, you would do this:
SWITCH 1: (assuming it is a VTP Server)
#conf t
#vlan database
vtp domain mydomain
vlan 2
vlan 3
exit
#interface vlan 2
ip address x.x.x.x y.y.y.y
no shut
SWITCH 2:
#vlan database
#vtp domain mydomain
exit
#interface vlan 3
ip address w.w.w.w z.z.z.z
no shut
After that, you will have to connect both switches using Layer 3 routed interfaces and configuring this connection as member of another VLAN, for example VLAN 4. Then configure one static route in SWITCH 1 like this:
#ip route w.w.w.w z.z.z.z vlan3
and the same thing on SWITCH 2:
#ip route x.x.x.x y.y.y.y vlan 3
And that should work.
