Reset it to no defaults, you just need to do what I exposed previously:
On the mikrotik, add VLAN interfaces hanging from the ethernet ports the Unifi are connected to with proper VLAN ids for the SSIDs they’re broadcasting.
If you have 3 UniFis, connected to ether3,4,5, you’ll end up with:
ether3
||_ VlanSSID1_3
|__ VlanSSID2_3
ether4
||_ VlanSSID1_4
|__ VlanSSID2_4
ether5
||_ VlanSSID1_5
|__ VlanSSID2_5
Let’s suppose router1 is wired to ether1, and router2 to ether2.
1.- Create two bridges, BrRouter1 and BrRouter2.
2.- Add ether1 to BrRouter1, and ether2 to BrRouter2.
3.- Add VLAN interfaces VlanSSID1_3, VlanSSID1_4, VlanSSID1_5 to bridge BrRouter1
4.- Add VLAN interfaces VlanSSID2_3, VlanSSID2_4, VlanSSID2_5 to bridge BrRouter2
From this point, You can consider SSID1 as if it were being broadcasted by APs directly connected to a virtual switch where router1 is also connected; same goes for SSID2/Router2.
You can manage the mikrotik with no configuration or IP addresses set, by using winbox (http://www.mikrotik.com/download), you’ll see the router appear on the neighbors tab; double click on its mac address.