Hi Linc,
How's it going?
It's been my experience with the Quark, that on 6S, it tends to cog more on startup. At least with batteries fresh off the charger. Into the run, as voltage comes down some, it tends to behave better on startup.
The Capacitor mod does seem to help this. I've noticed a big improvement on 6S compared to "un-modded".
If it thermals, that has to do with your motor drawing too many amps for too long a period of time as a result of high gearing or too high a kv motor, etc. Not necessarily your battery arrangement.
A lower kv motor should perform well on 6S through a Quark.
In thinking about this, I was usually using a setup that was more suited to 4S, but just thought I would switch to 6S to "see what it would do".