LIPO charging

Heres my question :

I have a MRC 977 super brain which charges 2 batteries at once. And it will do LIPO's also. I also have an HK battery medic which will balance up to 6 cells while charging or not. What I want to do is charge both lipos through the high power cables and wire my single balancer between the two 2S1P batteries to keep them balanced while charging. Will this work? Keep in mind that both A&B sides are different charging circuits.

All answers will be greatly appreciated.