Is there a way to configure a port for :
switch(config-if)# switchport trunk native vlan xx
using the port VLAN assigment in the LMS Campus Manager ?
If the port is already trunking, then the way to do this is with RME's Netconfig. If you have LMS 3.2, this is even easier since Netconfig includes a port-based template system. However, even with LMS 3.1 and earlier, you can create an Adhoc job to deploy this command to a given switchport.
VLAN Port Assignments can only be used on access ports.