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