I have something similar but dont use the controller.
So create two vlans vlanEE10 and vlanVF20
192.168.1.0/24
192.168.2.0/24
Trunk the vlans to the ethernet port(s) leading to the AP(s)…
You should have two routes already to the wans either because you have selected - use default route if using IP DHCP client etc.
OR, you have created two routes manually.
Add two tables
add fib name=useEE
add fib name=useVF
Add two routes
add dst-address=0.0.0.0/0 gateway=ISP1gatewayIP table=useEE
add dst-address=0.0.0.0/0 gateway=ISP2gatewayIP table=useVF
Add routing rules.…
add action=lookup-only-in-table dst-address=192.168.1.0/29 table=main comment=“Keep Local Traffic Routed”
add action=lookup-only-in-table src-address=192.168.1.0/24 table=useEE
add action=lookup-only-in-table src-address=192.168.2.0/24 table=useVF
The first rule is needed for any traffic that may be needed between the two subnets so it doesnt go out one of the WANs instead 
For vlan setup…
http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1