Separate two batteries getting charged by one charger with diodes?
Essentially you are asking how to charge a 3s2p pack.  The better answers will involve battery balancing.  A process which, in the most rigorous examples, involves extra wires to every battery terminal and a processor controlled charger.

Likely, the simplicity of using 2 independent chargers on 2 independent 3s1p packs outweighs the complexity of balancing a single 3s2p pack.  Even more so as the 2 independent 3s1p packs will have different power demands and therefor different charging histories.