we have a layer 2 cat-6506 switch (catos) uplinking to a layer 3 cat-6509 (ios). we're also required to portchannel the link between the 2 devices. So, we have trunked up 2 ports on the layer 2 switch and used vlan 4 as the native vlan. Do we need to place the ports on the IOS switch into the vlan 4 PRIOR to trunking them and defining vlan 4 as the native vlan?
From the portion of the config you've posted, I'm not 100% sure the 'mode' you are running.
If the 'mode' is not entered under a switchport, it runs in dynamic mode.
The dynamic mode can be desirable or auto, depending upon the switch you are running.
The dynamic behavior is unpredictable as you don't know when you are running trunk or access mode. It's best practice to always enter the 'mode'.
You can find out the 'mode' you are running with the show interface fx/x switchport command.
Based on your last post, it seems you were running in access mode, not trunk mode. Perhaps a failure in the negotiation with the remote peer.