By default all ports are configured as switch mode trunk, switchport trunk native vlan 1, switch trunk vlan allowed all. Since every possible VLAN ID is always available if you really want to prune VLANs on the trunks you can either create the VLANs in the VLAN profiles page (network wide -> VLAN profiles) if this feature has been enabled en add them to a VLAN group. Then you can easily add that group to each trunk ports you want to configure. Also, very important bit. Use the switching -> switchports page to control all the Meraki ports in your network and make sure they all have descriptive tags so you can always select multiple ports from multiple switches and configure them in 1 go and consistently.
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