I use a similar setup at home with RB5009 exposing via trunk some ports further down on L009 directly to WAN side of things (mainly for IPSEC connection to Azure and testing stuff).
Just look at it as another managed switch.
Define VLAN-WAN, setup your router functions on that interface instead of the real WAN port.
Define on which ports VLAN-WAN needs to be handled. Define your other required VLANs and access/trunk ports.
And that should be it.
VLAN bible for Mikrotik:
http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1