Quick question some of our switches have the switchport mode trunk command configured between the 3750 switches but other 3750 switches connected to our 6509 core switch do not have the switchport mode trunk command to permit Vlans from going across the swtiches instead it has an ip address and says no switchport what is the difference between does two. Is trunking used only for Layer 2 and L3 is used to route interface vlans?
You are on the right path. Trunking is a layer 2 function that carries multiple (tagged) VLANs across a link. The "no switchport" command (on supporting switches) configures the port as a routed (layer 3) port. The port will have an IP address assigned and route traffic between destinations.
What you are seeing is a common design practice. Access switches (switches in comm closets that connect directly to the end-user devices) will connect to distribution switches via trunk links. This allows the use of VLANs on the access switches to segregate traffic, and backhauling of all traffic back to distribution layer. At the distribution layer, the distribution switches connect to the core via layer 3 links. The VLANs terminate here, and the traffic is routed to its final destination.
As you suspected, the VLANs "terminate" at the distribution switch, and the traffic is routed from there.
This document gives several answers on frequently asked questions for PFRv3 channel state behavior.
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