How should I be using queueing when I am also using fast track?

RouterOS General
2

You can’t eat a pie and still have it. You cannot simultaneously put the packet into queue which you have bypassed for that packet.

http://forum.mikrotik.com/t/queue-tree-and-fasttrack-mutually-exclusive/107854/1

This can be inspirative although it might not help you much:
http://forum.mikrotik.com/t/fasttrack-friendly-qos-script/102401/1

Solution: not to use fasttrack for the packets you want to be queued in simple queues.