Orders

Orders are special commands the player can use once each turn at the expense of Command Points, which are earned at the end of every combat. By destroying more units in a fewer number of turns the player will receive more CP (the damage you have received will also be factored), though the number also depends on the Difficulty setting that has been chosen (harder difficulties will give you less CP)

CP is also used for special choices outside of combat, so you may want to be careful not to spend more than you really need.

It is not currently confirmed whether rescuing lolis gives you bonus CP.

CP
the standard reward after finishing a mission along money, CP are also a good judge of how well you have overcome the level. The faster and more you destroy enemies, the more that you'll get. They are the qualification of Captain Shields skills leading his units. Due to that nature, there are some options in the story that will require you to spend CP to choose them, so it's prudent to reserve a number of them instead of spending all in orders.

CP gained = (net money gained x 10) / (number of turns in combat + Difficulty modifier)

The Difficulty modifier is 1 in Captain, 2 in Hard, 4 in Space Whale mode and 0 on the rest

Net money is the reward money minus repair costs, the latter of which is based on the damage sustained during battle (losing one unit equals to 100 of repair cost)

Full Forward
These buffs are the same as the ones Claude and Chigara can provide, except they last longer and immediately affect every friendly units without any EN cost. The total boost to the players damage potential makes this order very attractive to allow for quickly wittling down the enemy which allows for even more CP gains at the end of battle, possibly paying back for itself and more. Cannot be active at the same time that All Guard, when one is activated it will overwrite the other.
 * cost: 750 CP
 * effect: All ships gain 20% damage and 15% accuracy for 5 turns.

All Guard

 * cost: 750 CP
 * effect: All ships gain a 10% to shield and evasion, and a 20% increase to flak for 5 turns. Units that originally have no flak or shield will not get the bonus of that category (so the Black Jack won't get a shield, and the Liberty will not suddenly gain flak).

Useful in certain situations for surviving large missile/rocket throws. Cannot be active at the same time that Full Forward, when one is activated it will overwrite the other.

Repair Drones
Very useful in a pinch, but remember you can only use one order per turn. After the Battle of Mnemosyne Abyss, it uses the repair drone consumable that can be purchased from the store (400 credits each, maximum of 8).
 * cost: 750 CP
 * effect: The Sunrider regains 50% of her maximum HP.

Short Range Warp
An exception to the rule, it lets you use any other order in the same turn. This means you can combine it with Vanguard Cannon or the others, or even make multiple uses of Short Range Warp (while you can actually use it as long as you have CP, take into account that the other orders will still make it impossible to use any other order in the same turn, so you can't use Vanguard Cannon and then warp, it's the reverse what is possible). Plenty useful, but due to it's "combo" nature it may make you lose CP points a lot faster than it's cost could imply.
 * cost: 750 CP
 * effect: Teleports the Sunrider to any space that isn't occupied by another ship.

Resurrection
A very useful order, just remember that the unit will be launched next to the Sunrider and with 0 EN it won't be able to move for that turn, so don't use it if you feel that you will end with that unit downed again due to a bad position.
 * cost: 2000 CP
 * effect: Launches a unit that has been downed at the battlefield at full health, next to the Sunrider, but with no EN for that turn.

Vanguard Cannon
It may be tempting to overuse this awesome weapon, but the high CP cost should give you pause and make you think whether there may not be a better time to use it.
 * cost: 2500 CP (4000 CP in Liberty Day)
 * effect: The Sunrider fires her main guns, dealing 800 unblockable damage to all units in a straight line up to 6 cells away. A store upgrade can be purchased to raise this to 1000 damage and 7 cells.