Hi,
This is my first time posting on the Mikrotik forums, so please be nice. I have only owned Mikrotik CCR2004 Routers for about 1 month now and I must say I have become a massive fanboy of Mikrotik (Cisco & Ubiquiti Routers are what I have most experience with). I picked the Mikrotik Routers over Ubiquiti mainly because they supported QinQ and it turns out I haven’t been able to find anything these Routers can’t do, even comparing to Enterprise Cisco Routers.
Anyway enough of my rant, I’ll get to the question. I am having issues wrapping my head around PPPoE + QoS. I have PPPoE-Servers (FreeRadius Auth) running on WA-RTR-01 & WA-RTR-02 (see attached diagram), which is connected to the L2 NBN Aggregation (My countries wholesale carrier). I want to setup shaping + HTB (Hierarchical Token Bucket) queues to all PPPoE clients. For example, I want to mark traffic sourced from 103.10.125.0/24 being sent to PPPoE clients and prioritize this queue over all other queues. This all makes sense to me if I am using physical interfaces, but with PPPoE it is confusing me. If I apply this queue to the physical interfaces that are connected to the L2 NBN Aggregation are they going to work? Because the traffic is inside an encapsulated PPPoE frame it won’t work? Should I be applying this queue to all PPPoE interfaces? Is this even possible to do while running PPPoE? I would really appreciate some advice.
Things of note, I don’t have control over the PPPoE client (CPE). If this isn’t possible I will switch my design to use IPoE instead since these queues are essential.

*Side note, the PADO delay on WA-RTR-02 is configured to 1000ms. This is the best HA PPPoE Server design I could find and it seems to be working well.