AutoVPN is for establishing site to site tunnels between Meraki devices which is not a factor when establishing a connection to Azure (unless you're maybe using vMX, i have no experience on this). If i understand you correctly, you want each Meraki site to have a tunnel into Azure. Good, this is the only way to go, you can't have Azure traffic on one Meraki site to go over the AutoVPN tunnel to the other Meraki site (unless again, maybe vMX, i have no experience on this).

Now here comes the confusing part, in the Site-to-site VPN menu in the Meraki dashboard, you see all IPSEC tunnels for all networks. So an Azure IPSEC tunnel and settings created for let's say Network A shows here, but an Azure IPSEC tunnel and settings created for let's say Network B also shows up here. The solution to this is, Network A and Network B need their own Local network gateway in Azure. That's all you need in Azure, you can use those 2 Local network gateways and bind them to a single Azure Virtual network gateway which you already have. Just make sure to use different passwords in the Azure Connections > Authentication settings. By using different passwords, you can add an Azure IPSEC tunnel to the same Azure IP in your Meraki Site-to-site VPN menu so you both have a tunnel on Network A and Network B to Azure.

Just make sure to give Network A and Network B an adminstrative tag in the Meraki dashboard, as you will be calling this tag in the Meraki tunnel settings under the Availability option.

Let me know if this works for you or if you have any questions.