I'm a level 54 Vygoid Builder, but, I don't know how I should build up my ship, what planets I should have or anything. I've pretty much been winging it. Winging it isn't efficient, any advice would be appreciated.

If you give us your current build and research, we could give you some advice. And also it depends on your goals and what makes you enjoy the game (pvp/nps/base combat/missions).

PvP-High hull and attack before rank 100, then start getting more defense

NPC- Attack is paramount, then energy (vital too). Defense and hull should be good enough so you don't have to repair often)

Missions- Energy, energy, and more energy...and some energy on top of that. NOTE: Don't leave yourself open to disables (keep weapons and hull at moderate levels)

100 or more cloak is very effective at low levels too. I don't know of many PVPers below rank 100 that had over 100 scan. If they can't see you, they can't shoot you.

Right now I've got 379 energy, 622 attack, and 35 defense. I'm more a fan of doing missions, but I don't want to be a punching bag.

At this point hull modules are more important than defense, as they provides more of a barrier for the deck size, cost, and research.

My ship has 250 decks, if you need to know that.

If your not in a legion already then you should find yourself a good legion as they will be able to help you out a lot more because they can see what modules you have installed and its quicker too.

We are currently taking on a few low level players just now if you want to join Storms Torment, just clikc on the banner below and someone will accept you in.

Which of the three should I join? I am in a legion but they're all about my level, on the other hand I've given them most of what they needed to upgrade their base.

You could always come to the Terranian Armada. We pride ourselves on helping newer players become DeathStars.