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You've probably worked this out by now but if you go into the Launch Manager (L), you'll see an option under each capital ship that says "Remain Docked". Click this and every time you dock your fighters/corvettes, they won't be released until you manually go in and release them.
Other things that you won't have picked up on in training:
Resource -collectors- can refuel strike craft. Very handy as I often use cloaked fighters to guard collectors, it's an unpleasant surprise for anybody wanting to take potshots at my resource ops. Heavy corvettes can burst fire. Hold Z and click on an enemy ship. and the corvette will charge up a shot and let loose. This works better on tight groups of enemies (e.g. Defenders) or peppering a capship with stronger fire. A Kushan Carrier is useless at attacking because it simply turns to face whatever you've made it attack. This doesn't help much when the cannons are on the sides of the ship and can't attack directly in front of it. However, you can get around this by simply moving the Carrier into enemy ships. It's strong enough to bash through three frigates, which is sometimes enough to give yourself room to breathe. Resource controllers don't repair, they only refuel. If you think you'll need to repair at a controller at some point then send a Support frig or a few Repair corvettes along with it.
There's plenty more I can tell you but the night draws late here in the UK. If there's anything specific you want advice on (ships, missions, general stuff) then let me know.
If you select your strike craft and then hover over a collector, you'll see the cursor change to the docking symbol. I don't think strike craft automatically dock with collectors, you have to manually tell them to.
On a related note, you can use the force fire command (ctrl+shift) to make collectors attack enemies. Their attacks are uselessly weak but they're good for irritating enemy collectors infringing on your resource patch, as if they're not set to aggressive they'll automatically turn around and head for a docking bay.