The biggest thing to get your head around is how things synergize between passives, skills and item mods. Once you now how to improve your skills this way the passive tree (aka skilldrasil) is going to look a lot less daunting and you'll know what kind of gear is best for your character. Planning out a build is going to be much much easier.
For instance, I've started a Scion on the Nemesis league because she's new. I'm going to use Spectral Throw throughout, which is what she starts with.
Since it's an "attack" (as opposed to a spell or trap) and a "projectile" (as opposed to melee), these modifiers will scale it:
Damage Modifiers: Spectral Throw is classified as an Attack and will benefit from x% increased Attack Speed but not from x% increased Casting Speed. It benefits from x% increased Projectile Damage and x% increased Weapon Physical Damage but not x% increased Melee Damage.
http://pathofexile.gamepedia.com/Spectral_Throw
Ideally you would want to pick up as many of these as you can on the passive tree. If you do that, you're going to end up in the Ranger's starting area on the passive tree and subsequently pick up a lot of DEX nodes. Which is just as well, because Spectral Throw is a dexterity skill and you will need more and more DEX level up the gem. Dexterity incidentally also opens up pure Amor-Evasion hybrid armour (STR-DEX), pure Evasion (DEX) armour and weapons like swords (STR-DEX). So an obvious path would be to specialize in that kind of gear and pick up additional nodes that synergize with those. I use two-handed weapons for my build, but I don't want to specialize until I find a really strong weapon. If it's a sword, I'll be picking up X% sword damage nodes. If it's an Axe, axe nodes and possibly one or two strength nodes so that I can use it. For now, I could be picking up X% two handed weapon damage nodes as well, but I'm forgoing those in favor of X% life nodes for now.
At this point it will become obvious that a Ranger might be a better start for a character using Spectral Throw. It's not necessary but something to keep in mind for future builds, since different classes can reach specific nodes much easier or earlier than others. Generally however, every class can do anything with the right build and gear, but the way there is going to look different. Often you'll level using different skills and gear and/or a passive build you more or less arduously spec out of.
There is more to it, but this is the basic approach. :>
