Perhaps a checkbox before the ship name would make you jump to the commander?
It's a good idea and has been suggested multiple times.
Meanwhile, back to your question:
And how do I know who is commanding what?
You have all the info already, just need to use multiwindowed mode. You know the name of the ships and on the fleet view you are able to see the commander in charge.
Also, in terms of changing, you can just select a more suitable commander and just assign it, which will relieve the current commander of the ship with the one you are selecting.
Don't get me wrong, far from ideal especially when you have thousand commanders to look at, however, what you are trying to do is already possible; time consuming, but possible.
