You appear to have two separate problems, with two separate solutions.
First off: Your 3D viewport camera settings. In Hammer, at the top-left corner of the 3D view, click on 'Camera.' A list will appear underneath of your cursor. Click "3D Textured." The view will appear more 'flat,' but the overlays shouldn't be flickering any more.
Note: this problem plagued me for months until I figured it out. I should write an article about it for the tutorials section... but that's for another time.
Secondly: You probably have a leak in your map (unless you are compiling without lighting, which in that case, select Run RAD -> Fast when you compile). A leak happens when your map is compiled: the compiler can't distinguish between 'indoor' and 'outdoor' sections of your map, so certain graphical glitches occur.
Give your map a quick lil' compile, then go back to Hammer. Click the top "Map" button, then click "Load Pointfile." If a file selection prompt doesn't appear, what will appear is a simple prompt saying "Load default pointfile?" (answer 'Yes'). A red line will appear somewhere around your map in Hammer. If you can't distinguish it right away, disable some Visgroups using the Visgroup -> Auto box on the right side of Hammer. Fly to the red line in Hammer, and follow it away from an entity to the dark abyss. Close up any gaps you come across, and once there are no leaks, you should be good to go.
If these steps don't do the trick, or if you have any questions, we'll see if we can resolve the issue.
and try again
