"Create each subnet on site B separately with separate VLANs"
 
I don't understand this. Is there more than 1 way to create a subnet and VLAN? Or does this just mean I need to have more than a single subnet and VLAN in the network? Because that's a given.
 
"Only include VLAN99s subnet in the SD-WAN and have the default gateway of VLAN99 as the MX,"
 
Which MX? Site A or Site B? VLAN99 only exists in Site A and I have included only that in the SD-WAN VPN. Is this correct bellow?
 

"other VLANs have interfaces on site L3 switching"
 
You lost me here. Why do I need to turn on L3 switching? I've never dealt with L3 switching on meraki. The last time I dealt with L3 switching was on a cisco catalyst years ago. 
 
"Have site B as a spoke with default gateway as site A"
 
Is that the checkbox on the Site to Site VPN page?

 
I appreciate the help.