Logically, the covered area should be omitted. Personally, I just don't color it, although there may be a time in the future where I might draw a character whose eyes might be completely covered and I might not draw them at all.
Sketch everything out, eyes and all, draw in the hair over the top, remove the sketchy part of the eyes behind the hair. I'm realistic about it. I hate cartoons/animes that show eyes through the hair like it's some kind of see thru object.
i used to draw and colour the full eye over the hair, then i just did the outline, now i dont draw any part of an eye thats covered by hair xD i do draw the eyebrow over the hair still though, if any part of the eye is visible out from under it