Check various guide sites for champion-specific runes/masteries to be as customized as possible if you have strong favorites.
In general though, use the following:
You have two free rune pages, and runes are expensive (so use runes that work on both pages):
AD page: flat AD marks, flat armor seals, MR/level glyphs, Attack Speed quints (if you main adc) / Armor quints (if you main top) / MS Quints (if you main jungle or play everything)
AP page: magic pen marks, flat armor seals, flat MR glyphs, flat AP quints (if you main AP mid) / MS quints (if you roam from mid, e.g. Ahri, Zed, Kat, etc...)
You should also note that there's a 2 for 1 rune page sale (costs 6300 IP per page, so you'll get 2 for 6300IP, at your current amount you probably can't afford to get any, there are typically 1-2 of these sales per year though so watch out for the next one) and 30% off T3 runes, both starting on Jan 22. So WAIT a few days before buying your runes, and buy all you can afford then.
You'll want more rune pages eventually. You're more than welcome to search my profile in game (go to your friends list and click the magnifying glass and search my name) to see my profile, go to the runes page, and view my basic set up for 2 rune pages (go before January 22nd) and soon 4 or 6 rune pages (I'll be adding a lot during the sale, I've saved up over 20K IP).
To go in to more detail on runes:
Once you get a few more pages, here is what you'll want to focus on (at least what I'm planning to get):
- An ADC page: AD marks, flat armor seals, MR/level or CDR or Mana Regen Glyphs (or a combination), and Attack Speed Quints (or Lifesteal or AD)
- An APC vs AD page: MPen marks, flat armor seals, Flat AP or Ap/level or MR/level or CDR or CDR/level or Mana Regen glyphs (or a combination), and flat AP or MS quints
- An APC vs AP page: MPen marks, flat health seals OR health per level seals (or combine with some flat armor seals if you expect a strong AD jungler), flat MR glyphs (or AP or CDR or mana regen glyphs or a combination), AP or MS quints
- A Tank page: Armor marks, Armor seals or Health seals, MR or MR/level glyphs, Armor Quints