1) As far as I know, the main method of getting energy credits is selling stuff. Either into your replicator, to a vendor at Stardock, or to other players through the exchange. I've always had plenty of energy credits just by selling the loot that comes my way.
2) Each promotion you get one free ship. If you want to try out more ships, you'll have to purchase them.
3) If I already have the comodities from loot, I'll turn them in. Otherwise, I've just been leaving them on my mission list to come back to later. Not sure if it's really worth it or not.
4) Focus on the stuff you enjoy doing. There's no wrong way to go about it.