The natural ship AI is very good, and will produce battle line and flanking behaviors on its own. You usually won't have to give it any commands at all, unless you want it to do something weird. If you're new, just focus on learning to pilot your own ship and don't bother giving orders. If you don't know how to correctly fly and position your own ship, you won't be able to give effective orders to your fleet.
Before you start giving orders, you need to know how the command channel works. While you have the tactical overlay open, any order you give will open the command channel for about 10 seconds. Further orders given while the command channel is open will not cost command points. The command channel will close once you close the tactical overlay, or after the time period has elapsed. To get the most use out of your limited command points, you should give orders occasionally and in bulk, then focus on piloting your own ship.
The Full Assault order forces all your ships to Reckless personality, so I'd avoid using it unless you're certain you can win the fight and just want to get it over with. The Escort order will effectively prevent the assigned ship from engaging the same targets as the escorted ship, in favour of covering the escorted ship's flanks and rear. The Eliminate order forces the assigned ships to Reckless personality and to single-mindedly engage the tagged ship until either the assigned ships die, the tagged ship dies, or the Elminate order is canceled. The Avoid order makes sure that your fleet will stay well away from the tagged ship, and is mostly useful for having your fleet avoid a big slow thing it can't kill yet until you've taken out most of the rest of the enemy fleet and can set up a surround. All of these orders are situational, and probably shouldn't be used in every single fight.
Defend orders are used to force your fleet to create a battle line in a specific place, if for some reason you really want to set up in a particular location. Set up 2-5 of these in a row, and your fleet will congregate around them. However, they won't move away from the defend orders if the enemy fleet pulls back, so after the engagement is joined I would recommend disabling these so your battle line can move forward and keep the pressure on. Task force orders will have specific ships move to a specific place, mostly I use these to keep vulnerable carrier ships behind the battle line and away from the enemy, but again they won't move away from the order location if the enemy pulls back, so you have to pay attention and disable the order once the battle line moves.