Runes feel really intimidating at first. I remember when they came to server 3. I was like....what do I do with all this?? I thought there was no way I would figure it out and wasn't sure I even wanted to. But then I started getting killed by toons with runes (see that rhyme there? lol) and thought I'd better start figuring it out.
Go here and read the public guide by PB to get a feel for what the different things mean. Great place to start. Then I recommend starting with getting free runes from wood shrine to just to get a couple so you see what the runes look like.
Save up your runicite! It goes quickly. Later I believe it's worth it to get 2 runes with Stone Shrine so you don't have to sacrifice the few runes you have initially received in order to level up by fusion. The difference between 1 and 2 star runes makes quite a difference imo.
Got a bit carried away...basically now I totally love runes. They bring an additional strategy to the game that perked it up for me at a time when I was tiring of just gear and enchanting. I have some rocking heroes that would not be nearly as good without runes.
Use this stupendous rune helper and you'll be fine. It's really trial and error at times but this script helps a whole lot!!