Is there a way using SDL to make a mouse click register only on the "top" surface? I'm trying to make a simple pop up menu which I have done successfully, however when I click the menu options my click registers both in the "top" surface (ie the menu) and on the game map underneath it. I've read through the documentation and the only thing that made any sense was making an overlay, but almost every mention of overlays that came up in google involved video of some sort, and that is not what I am looking for at all.

you will have to handle this yourself manually like extralongpants suggests. There is not automatic way for SDL to handle this.