Exactly what you said. My basic AI command strategy is to try to rotate ships that are at high flux to the backline/less exposed position to be relieved by ships low on flux. The way these powerful capitals die is being swarmed and unable to back out.
Accomplishing this requires a couple of things. First of all no ship may ever be left alone. Ships should ideally be in range of their companions (Odyssey is generally an exception to these rules). Second, you must try to be aware of the location and flux level of each ship. Third, ships are not allowed to be directly behind each other as this blocks retreating, unless that is specifically what you want to do.
Another thing is just trying to roll with the AI rather than order it to go against its inclinations. For example you may notice sometimes I order something, look at the ships, then immediately cancel it. That is usually because I notice a ship's heading and intentions and change the order to better align with those. You eventually get a feel for it and try to guess what the AI is doing.
Then there's the commands themselves and unfortunately it must be kind of learned ship by ship what they do. For example on the Onslaught I can use Retreat to signal "fix lateral position, head directly south". This is not permissible on Astral or Odyssey because retreat command causes them to drop shields.
If you can bear to watch it, I think the Gigacannon Executor video is my best command work and also fairly generic as there are no special AI meanings to the commands for that ship unlike say Astral or Odyssey.
I actually think that if you do all this to avoid its pitfalls - namely keep a line of battle so each ship can fire and back off without blocking each other, and guide the ships in harmony with their natural movement so to say - then the AI does a really good job of the micro, gauging when it should back off etc, other than the bugs to do with orders. Your job is to have a plan, to be aware of the overall situation, to issue orders to pre-empt developing dangerous situations like Fulgent swarms or excessive pressure on one ship, to occasionally tell it to focus an important target, and to untangle the inevitable knots in the battle line effectively, and the AI can do the rest.