Hotkeys, and where you put the ships. If the ships are on the front line and mixed in with other ships. They are usualy already on my hotkey's. So I can just select the whole group to go from low to full power mode quickly. And its only these groups that will go into low power mode. Except for my rear guard, Somtimes I will have ships back a bit out of combat on a different planet. (maybe a lowertech group, or a high energy group). but basicaly all the planets ships will be in lower power mode, so its easy as selecting all the ships on the planet and putting them into full power mode if needed.
You just gota watch how your managing your fleet, make it easy on yourself. If your going to put them into low power mode, put whole groups, or whole ship types into low power mode, not just a couple. This way they dont get all mixed up. Organization.