Having one Bridge for me simplifies the setup.
Read through this source for the best approach Ive seen.
http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1
I have multiple vlans, multiple managed and unmanaged switches and multiple APs (two cap acs and others).
I use one bridge on any mikrotik device. Only the main router handles the DHCP.
In my firewall rules (both forward chain and input chain) I mostly use allow rules and a last rule of drop everything else.
Therefore if I do not explicitly allow traffic at L3 between vlans, it does not occur.
Since vlans are blocked from each other at L2, the only way they should see each other is via the firewall rules.