It depends on your threat model and general situation, but you’re probably better off with the second option (assuming that by “2 instances of Whonix” you simply mean multiple Whonix VMs). It’s closer to the intended design and is well-trodden ground, so you’re less likely to run into weird problems that no one else has encountered before. Also, depending on your needs, the first option is probably unnecessary, more cumbersome, and probably won’t grant you any meaningful benefits over the second option.