This tool will only be able to configure Cisco routers, not switches.
It means you will have to configure NetFlow manually on them.
Here is good doc to start from for the 6509 one: Enabling NetFlow and NetFlow Data Export on Cisco Catalyst Switches
Now that I have set it up and can see a check mark under sending Netflow...how can I see the charts or data being collected?
Within the NTA Settings in the admin area, at the bottom you will have your list of nodes and interfaces being monitored. If you have not designated the node & interface to be monitored for Netflow, you can click the edit button and enable it in the following screen.
Also in the Netflow Summary page, by default there is a Netflow Events section, which will inform you if it is receiving Netflow packets from an unmanaged device or interface. From that point ensure you have the Node and Interface added to Orion and that you have enabled it in the above section of the admin area.