Question on magic pen. runes

So, these past few hours I've been trying to increase my base knowledge of the game, so that i can hopefully get better at it. (Hah..right...) Anyway, I was wondering whether Magic pen (runes) would be more beneficial against champions with scaling MR or flat MR (Champs that gain MR per level versus champs that don't). I know a lot of it also depends on your champion (Those who benefit from Mpen items in-game (Zyra, elise)), but it would help decide whether or not to take mpen glyphs in place of MR or AP on champs with low scaling abilities, etc etc. I'm also thinking about whether or not i'm trying to win lane early or scale into the later game. Basically.....what is best for each situation?

Info from higher elo players is preferred, but any opinion is welcome~