I have 4 VLANs set up for our network. VLAN 50 for Servers / Firewall, VLAN 100 for Workstations, VLAN 150 for VOIP, and VLAN 200 for WiFi. What is the best practice for setting the trunk links VLAN membership? Is there a difference between the "trunk native vlan" command, and "switchport access vlan XXX"? Should I make the native VLAN for trunk links the Servers VLAN, or a completely separate VLAN?
A trunk's native vlan is the vlan to which untagged traffic belongs. switchport access applies only to ports in access mode -- while in trunk mode, those commands do nothing at all.
Which vlan is "native" (and this not tagged) is a matter of personal preference. You could leave it at "1" and not allow "1" on the port (switchport trunk allowed vlan)