How to set one region over the other (and not beside it) in Omega theme?
The side bars are used to create columns and not for placing it one on top of the other.

If you want a single column then you would go for one of the three. If you want two columns go with any two of them and if you want three columns go for all three. 

As for placing contents one on top of the other the blocks should be used for that. Let us say you have two blocks one to show the latest articles and another to place the login box and you want the articles to be on top of the login box then you would go with one of the side bars and content and place both the blocks in the same sidebar and arrange it as you would want it.