I am wanting to connect the Cat 6509 to the N5K using 4 - 1Gb ports channeled. My question is - do I need to configure the Interface Port-Channel XX on both switches and apply to the interfaces?
Configuring the port-channel on N5K shoud not be any different than in other Cisco Cat switch. In case you configure vPC, you can check out the following doc as a referenece.