I sighted in my Eotech 512 at 100 yards the other day and noticed when I wanted to move the recticle up I had to turn the adjustment screw in the "down" CW direction. Is this normal or am I just missing something here? The dot is sitting right on top of the front post which I zeroed at 100 yards.

Just like the instructions state, adjusting the set screw DN moves your POI down, UP moves your POI up.

What exactly is cowitnessing. Is it when the recticle, rear aperature and top of front post all line up?

Co-witness is the ability to see your iron sights through your optic if your optic fails. There are two types of co-witness, absolute and 1/3.

1/3 co-witness places the iron sights in the lower 3rd of your optics Field Of View leaving more room to view your target.

Absolute co-witness places the iron sights directly in the center of your optics FOV leaving less room to view your target around the irons.