One of the most important thing to keep in mind when building space ships is to keep to a single energy type and also to pick a single arc type.
What I mean here is all energy weapons should be the same, whether phaser or tet or whatever you like, and all torps should be the same type as each other.
As to the Arc comment, there are two primary arc types used in this game. Forward firing ships, ussually escorts using cannons, which are very high damage in exchange for only being able to shot a limited (90 degree) area or Broadside in which you fly sideways so your fore and aft beam arrays can fire at them at once.
Nah, this is a rather challenging game in many ways, with a lot of complicated options to master. Certainly, it has taken me months of playing, experimenting, and reading to work out my own methods for the game, and there are still people I see from time to time who can blow me away in terms of capability.
Take it slowly. Fortunately doffing is something that you can explore in time - you might then think that you've wasted so much time, but at least your head doesn't explode!
There aren't many Holy Grails in this game. By that I mean that, as an example, TacPaddy and I have a KDF tactical char. His build is different to mine. He works really well in one ship, I don't get on with it at all. I prefer another ship that he just doesn't sit well in.
Don't try to be a great man. Just try to be a man, and let history take care of itself.
Many people will disagree with me here - but concentrate on 1 type of play, 1 ship. If you're a tactical captain, think Dual Heavy Cannons in an Escort type ship. Then when you're looking at your build, think damage, hitting and awesomeness. A lot of the descriptions are very good at helping you think if you need something. Threat Control means you're more likely to pull agro - super for a tank, sucks for a tac.
Just take baby steps and get used to one thing before piling more on the plate! It's supposed to be fun :p