Most runes aren't worth empowering. Not only that, but if you empower all your runes, you won't want to fuse them, and fusion increases power a lot more than empowering does.
My general rule is, unless a rune starts out purple or orange, I don't empower it. If it is purple or orange, I only empower it if it's really useful for a hero. For example, Starting Energy, Movement Speed and Expertise are some of the better stats. If one of those is a primary and one is a tertiary on the same purple or orange rune, I'll often empower up to +12. Or if a specific hero likes Cooldown Reduction (thief, ninja, storm drake etc) or something, I'll empower runes as I need them. I never go around empowering for no reason.
Since the color changes are confusing and make me forget how good a rune is (yeah, I could do a bunch of math to figure out what color it started out, but I'm way too lazy for that -- I started to make an online calculator once), I usually empower purples no higher than +11 unless they're really good. That way, they stay purple, so you can tell the difference. Similarly, if I just can't find a good purple or orange for a hero, I'll temporarily give that hero a blue, and empower it up to +8 to keep it from turning purple.
Finally, you shouldn't have to do 5x, then 1x, 1x, 1x. You can do 5x, then 5x, then 2x.