If I do understand the bridges, you have two option.
- Bridge vlan-filter=off (old way)
This is the old way and you use one Bridge pr VLAN - Bridge vlan-filter=on (new way >=6.41 software.)
With this you can use one Bridge that handles VLAN tagged packet
See my graphical attempt to learn how it works here:
http://forum.mikrotik.com/t/sofware-vlan-bridge-on-ruteros-explained/122534/1