Percent runes are going to be good for champions where you actually buy more of that stat. Example being buying % Health on say Mundo. You're going to be building health somewhere, so for every health purchased, you get more out of it.
Flat runes are the opposite. Jax being a good example of this. You might buy health somewhere (Triforce), but it's certainly not a core component of your build. Therefore the flat health is going to be a lot more effective than additional %.
Following that logic, Flats vs Percent are a lot like Flats vs Scaling. Flat runes are going to be more potent in the early game, where the Scaling and Percents are more significant later on.
Best advice though, try both and see how they feel. It'll give you a much better idea of when and how to use each.