上午 vs 下午

If i asked someone, "What time is it?", and they said "on top of noon (上午)", I would definitely think that is is AFTER noon. Likewise, if someone said "beneath noon (下午)", I would think it is BEFORE noon . But in Mandarin, it is the opposite. Does anyone else find this confusing, or is it just me? haha.

It is not a confusing, it is  naturally.

in any of your schedule lists, AFTER noon is always under the noon.

Well...I do believe we normally don't translate in that way.

Instead of drawing the timeline horizontally :

上午             |            下午

before       (noon)        after

you can try to do it vertically

上午              before noon

                    上(up)

----(noon)

                    下(down)

下午              afternoon 

Hope this can help! :D