Change your other Cisco devices to using MST before you integrate Meraki. The Cisco Enterprise per VLAN RSTP implemention can cause all sorts of issues when used with Meraki.
I would go with a simple MST design with a single area (so you can simply issue the command "spanning-tree mode mst" and nothing else). I would also do this since you are phasing out the old Cisco Enterprise kit.
Try and avoid layer 2 loops in your design while you have both sets of kit deployed.
If you have much multicast in your network use the beta software 10.18 (or better if it has come out by then). Otherwise 9.36 should be fine.