Transparent AP Setup with VLANs

Correct,
Never used that MT device, however ROS is pretty standard.
Basic is to use a bridge to handle all the vlans and wlans.
Identify the vlans on the MT device.
Set up bridge ports and bridge vlans appropriatelly
Set up wifi appropriately.

This guide may be helpful in that regard.
The only tricky things is you are saying wireless AP, meaning it gets signal wirelessly and then also sends out wifi to its own clients.
Do you have two separate radios (one receives traffic from the main source) and the other used to TX/RCVE to local devices??

http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1


BASIC CONCEPT
Take existing bridge or if none make one, would be to change name and nothing else (keep defaults). After you fill in the rest of the stuff below (as per the guide, its just a rough swag), then you go back to the Bridge and select vlan filtering=YES.

BRIDGE-WLAN (keep default vlanid=1)

bridge ports would include

  • INCOMING WLAN (trunk port) (ingress filtering=yes)
  • LOCAL WLAN1 (access port) (only priority and untagged packets)
  • LOCAL WLAN2 (access port). (only priority and untagged packets)

tagged: BRIDGE-WLAN,INCOMING WLAN, untagged: LOCAL WLAN1 vlanid=10
tagged: BRIDGE-WLAN, INCOMING WLAN, untagged: LOCAL WLAN2 vlanid=20
tagged: BRIDGE-WLAN, INCOMING WLAN, vlanid=5 (assuming this is the managment vlan and the LAN subnet which gives your MT AP, its LANIP address).