Hi theworst ping,
I take it you followed @iddqd instructions at How to use the cake queue management system on the Turris Omnia about how to get cake working under sqm-scripts? If not please do so and re-test whether that will not already fix your problem.
SQM allows to instantiate multiple shapers (on different interfaces), but the catch is that if instantiate multiple independent shapers on internal interfaces, you will either massively over- or under-use the WAN bandwidth, the former leading to bad latency under load and the latter to poor speedtest measurements and bandwidth utilization. Setting up a shaper that will treat multiple internal ports differently is possible, but not easy, so avoid that if possible.
My approach would be to try to figure out where exactly your “lag spikes” are coming from and then try to fix that root cause…
Best Regards