Flat CD for glyphs because it is equivalent to the per lvl one at lvl 13. The early-mid game advantage outweighs the slight end-game advantage for the most part. Also if you spec 9/0/21 (you probably wouldn't spec this as twitch) you get 9% cooldown reduction. 9x flat CD runes = 5.85% cooldown reduction, so with a golem buff you'll be at the cap of 40% CD reduction.
For HP I would definitely go with the health/lvl. The flat amount is laughable and the per level one is better once you hit lvl 5. If you want early game HP, go with quintessences. 3x flat HP quintessences will put you at +100 hp, a significant chunk in early game.