When I have run a LAG under SwitchOS (on a VLAN trunk), I have set the VLAN and VLANs tabs to match each other for the two ports that are part of the LAG - it worked that way. I have never tried any other way and there is no setting on either the LAG or VLAN tabs to reflect that a specific VLAN is on the LAG - only the ports.
This was done on CSS326 switches.