Maybe part of the issues is the usage of orders is a bit viral, in that once you start, you have to do it for all ships, all battle. And if you do stop mid battle because you run out of CP, you'll likely get a behavior you really didn't want. For example if you order multiple groups of ships different kill targets, when one of the targets is eliminated the newly unordered ships will try to attack the other targets (rather than ones nearby), unless of course you have command point to burn to fix this issue, at which point the process continues until you run out of command points. The result of all of this is you can't really "play the game with this system" unless you're very careful or have some skills. Or what I do most of the time is just order all ships to follow me and cannonball into the enemy lines.
Maybe I'm doing this all wrong, I would love to know how to deal with the above scenario.
Viral is in an interesting way of putting it, and I can see that. Starsector has a fairly unique (as far as games I've played) command system. Most "command" type games, say an RTS like Starcraft or something out of the total war franchise, will tend lose every time if you don't issue any orders, and in fact other than shooting at things in range, your units will sit there until destruction. Issuing orders is the only thing you do and units tend to perform those order to a mindless degree (baring morale type mechanics). You also have to issue far more orders during a typical fight in those types of games than you do in Starsector to have similar levels of success.
I guess one question is, are you trying to always have engage orders up? I don't generally feel a need for those to get the AI to engage. Say you have an initial set of orders to get your fleet arrayed like you want, and assault some objectives. That's 1 CP at the beginning. Now you've spotted the enemy. Cancel waypoint/defend orders (free), and issue 2 priority engage orders on two capitals on opposite sides, and the rest of your fleet on search and destroy (the ones you don't want focusing on the engage targets). That's 2 CP total so far. Then when one capital goes boom, you issue another set of search and destroy to the successful ships, and that's 3 and your done. Unless you're issuing like 5 engage orders, you should have sufficient CP from the beginning of the game to do that each time. The game is trying to make it so you don't need to tell every ship every time exactly who to engage.
If you're trying to use waypoints and engage orders to get ships to engage exactly how you want every time your ships are near enemies, then I can see running out of CP. But that apparently is a design decision for the game. To force the player to be somewhat hands off. I can't see any other reason for command points other than to encourage you to close the map screen and to pilot your ship rather than playing fleet admiral 100% of the time.
If you prefer a more RTS and micromanaging style, which is a perfectly reasonable game preference, I'd suggest modding the game to give yourself more commands points and a shorter regeneration time for them.
You can easily modify the starsector-core/data/config/settings.json file, specifically these two lines:
"startingCommandPoints":5,
"baseSecondsPerCommandPoint":120,
It will change the nature of the game, but if you're not enjoying the fact you have limited orders, it's one way to change it more to your liking. It allows you to play the game much more like Starcraft, where each unit can, and always needs to be issued specific orders (to compensate for the changing situation and the fact you're giving very specific orders in the first place). If you do this, I highly recommend using the ctrl groups for faster selection of your ships. If you tend to command your frigates to do captures, setting them to say group 1, and other ships to 2 and 3, lets you hit 2, search and destroy (S key), 3 S, then 1, right click on capture point. Since the game remembers ctrl groupings from fight to fight, it can be a very quick way of setting up rather than individually hunting and clicking on the ships you want.