I keep trying to export my character sheets with the ability scores on top of the modifiers. It seems to come out the other way around every time even though the online character sheet shows the correct orientation. Any suggestions?

Edit the character.   On the home tab of the edit there is a place to that setting.

I have no problem changing the setting, it just doesn't make the change when I export the character sheet. 

The exported character sheet does its own thing that doesnt check your settings. Basically, it already decided where everything goes and grabs values to put there.

If you want it to look different, you have to edit it after the fact.