Why does my eye ache when i wake up, but then goes away when i close them again.

Likely dryness: you have not been blinking over night and the eyes have dried out a bit. The tear film needs to redevelop and that may take a little while first thing when waking.

Eye slightly open: Your eye may not close all the way when sleeping, so it dries out. You could try putting in an over-the-counter gel drop or gel in your your eye bedtime to coat your eye all night so you don't have pain in the morning.