Though it doesn't happen often, DJive is kindof wrong here. The vertex tool is not needed. If you need to make a quick hole, door, etc; you can use the cut tool for basic squares. Though he's right about not carving stuff. 3d skybox 101, in a few basic steps;
First select the borders of your map, brushes only. Copy/paste. Now around those borders create the 3d skybox. This means the floor of the box is underneath the pasted geometry, and the floor that people see is level with the pasted one. Add sky_camera to the center. Delete the pasted geometry and resize everything. voila. Spaceweasles made a good tutorial here;
http://tf2maps.net/showthread.php?t=116