In general, the static runes give you a better early game boost while the per level runes give you better end game stats. It's helpful to determine what level the /level runes will catch the static runes when making a decision (runes that catch up to their static counterparts quickly tend to be better). Which one is better depends on the runes and your personal preference/playstyle. Use static runes if you find yourself needing an early game boost but feel good late game, /level runes if you find you need a bit of an assist late game but are doing fine early game, or a mix if you are somewhere in between.
You may also want to pop on over to the guide section. Most champion guides will discuss rune selection and reasons for picking those runes, in addition to occasional discussions about the runes and which ones are better in general.