Relax, it's not as bad or as complicated as you think. Its worse...nah only joking.

But truly, why have they gone out of their way to make it all like this? Well once your in the groove, reverse engineer your point and you'll understand why.

Let's get started; First off Reddit is a fairly good place to look at builds, how to's , tactics , whatever it is your after more often than not you'll find the answer here.

Let's assume you have a ship geared appropriately ( as in your warp core is not slotted in your tac slot...OK you cant do that but you get the drift..) so for arguments sake you are in an escort as a tac captain. Choose one weapon type and variant; so for example lets go with dual heavy cannons and anti proton. Why? because your boff skills in your tray effect your ships gear. And your consoles effect your possible damage output. For example using bfaw with the afore mentioned set-up wont do diddly squat to your cannons output. However slotting CRF obviosly will. Umm right - bfaw = beam fire at will ( good for beam weapons) / crf = cannon rapid fire (good for cannons). Mkay..K.

Space set next...engines, core, deflector and shields. To start with slot anything in there but of course different types of space sets provide different possibilities and boons. In this case we want something dps focused with some durability as escorts can be squishy. Having the deflector, engines and shields from the same set provides set bonuses which can be nice. A good one to start with is the borg set, its fairly beardy and looks mean =) more importantly its fairly easy and quick to acquire via the rep system**.

Other items are self explanatory, sci consoles provide additional sci skills and powers, such as increasing how much power you can take from an enemy. Engineering slots give you more armour, turn rate etc. Tac slots boost your dps. in this case we would slot anti proton tac consoles to push our cannon damage up. So these are basics and if you didn't know these already you have some idea now. If you did then that was 2 minutes of your life you're never get back and 5 minutes of mine writing this shit =p

** The rep system. Hit 'U' on ya keyboard, go to the rep tab. Doing specific stf's or missions will grant you rep marks in the relevant faction, this builds rep and grants you new toys to melt your enemies with as you progress. They also open up additional skill - traits for you and you crew to utilise, such as additional crit chance for example. Which order you do these in is up to you as a) you may hate certain missions / stf's therefore look else where or b) gaining rep in that faction does not primarily benefit you and your ship.

The rep system is straight forward enough, but be ready for the grind.

Next think about hitting the delta quadrant and level to 60.

Captain skills, best thing to do is look at a similar toons setup, then ask specific questions if you have them.

So here's a link to a post on here that I looked at the other day, forget the numbers and the fact that its well geared. Just look at whats where and then ask why if it's not obvious. http://www.reddit.com/r/stobuilds/comments/2w8oyk/4060k_phantom_dhcs_with_surgical_strikes/

As for upgrading and R&D I would break this into 2 parts. R&D gives you the ability to craft gear and items as well as the upgrade components you need to upgrade gear. Simply upgrading items can be bought (costing both EC and dill) and depending on how much you spend increases your chance of getting some big boosts. But this side of things can seem to be complex and non intuitive so I would look at this:

http://www.reddit.com/r/stobuilds/comments/2ilks7/a_quick_guide_to_item_upgrading_essential_for/

It helped me so it stands to reason it will help you....maybe.

lastly tactics for actaully playing the game. When you get into the rep system and chase points there in you will be doing the STF's to get the rep marks. You really should...no you must look at the tactics for that specific raid..here youtube is your friend as many friendly players post vids on how to do these more complex missions.

Still need help, just ask and a friendly redditor no doubt will chime in with their wisdom.