If you really feel you need runes, like he said, get t1's. Do not get T2's, they're too expensive and you'll replace them with T3's at some point Do not rely on the combine system, it's completely random.4
I would focus on trying heroes until you find one you REALLY like and a willing to play a long while until you build up the IP to buy runes. Those runes won't help you much or at all if your not good with your hero/don't really like playing them.
To answer your question about runes, You can only use a individually purchased rune once per set up. So yes, you must be each rune multiple times in order to fill all 9 slots (3 for quints). However, you can use the same runes across different rune pages, so if you want to use the same runes in a different setup, you do not have to buy another set.
When you do start buying runes I would get a standard set:
Red: 9 Armor pen and or Magic Penetration
Yellow: 9 HP/Lvl or Flat Dodge
Blue: 9 Flat Cooldown Reduction or Magic Resist/lvl (i pref CDR but some people like MR)
Quints: 3 Flat +32 flat HP
As colloquial said, get quints first, and probably work your way up that list with Magic and then armor pen runes last (though really, the order doesn't matter, just get quints first as they provide the highest benefit for the lowest cost, I say magic and then armor pen last because that way the runes you buy will be useful no matter who you play)
If you switch between Armor pen and Magic Pen, you will have a rune set that work with every possible hero in the game. You can specialize them more if you want, but this is probably the most cost effective setup.
Edit: I would still go Flat HP over CDR quints becuase:
1.) The benefit is much more noticeable, 100~ Hp vs 5%~ CD reduction at the start, the HP is more impactful.
2.) Not all heroes can use that 5% CDR. If you're a hero that stacks CDR, the 5% from blues alone will probably juuust cap you with 1 item, with 10% you're probably going over the cap, making it useless. Even if it doest, if you're not playing a CD reliant hero (let's say master Yi), that 5% does absolutely nothing for you, but defensive that 100 HP could save your life at the start of the game and offensively, that 100 HP could allow you to have the confidence to early dive for a kill and be able to survive (I recently built a page w/o HP quints and immediately missed it in my first game because I missed a kill I would otherwise easily have dived for, but couldn't becuase of my lower HP pool.)