just like you said, set your trunk with native vlan 999 and allowed vlans, the vlan you need over the trunk.
nothing different than on a catalyst.
as example on my lab setup ( here i'm using the vlan 32 as native wich is my management vlan for meraki, this makes it easier and quicker to add devices ( yes i know, it's not secure to have your management network as native on uplinks with dhcp enabled 😉 ) but you get the idea
![meraki_uplink.JPG meraki_uplink.JPG](https://community.meraki.com/t5/image/serverpage/image-id/10433iA70563E9C4F1FE7E/image-size/large?v=v2&px=999)