Welp, you're supposed to practice a bit without runes/masteries/items either way to improve your CSing. I can tell you for a fact even LCS pro players do that if not daily at least a few times a week. Early game CSing is so important but for some reason people ignore it.
I started playing ADC this season (5 years of support with very few jungle/top/mid games and close to 0 as ADC) so I had the mechanics of a potato. I could CS though because I trained for ~50 games(trying to get perfect CS in the first 10 mins) in custom games. Getting a BF sword at 6 minutes while the other guy has a pickaxe or vamp scepter simply made me auto win the lane because a kill would come shortly after. Not to mention it makes CSing 100 times easier because even if you fuck up your wave manipulation (custom game practice helps with this as well) you can simply kill a creep from half health.
The whole idea behind this kind of training is that you'll be consistent so you'll have close to perfect CS even if you are behind, equal or ahead.
On topic, yes runes are the most important thing in the game to get. If you're a good player you can get Challenger with 2 rune pages but you pretty much can't do shit without them.