Mirror Modifier

This problem is really bugging me. I bought The Essential Blender and just finished the chapter about armatures. I wanted to make a character model so I can create an armature for it. So I found this tutorial:

Modeling A Lowpoly Character - http://www.montagestudio.org/Tutorials.html

I started with my default cube. Used loop cut to split it in half (The guy in the video doesn’t say to do that but I noticed he started with a split cube.) Then I applied the mirror modifier on the X-axis with Do Clipping enabled. But when I enable the edit cage I get extra faces on my cube. And then when I extrude my cube outward (to make torso area) I get another set of faces extruding toward the center. I don’t want that to happen, I was only trying to extrude them outward. Also, my edge loops are all messed up. Some areas of my model are not part of the loop when they are supposed to be.

Im just starting out with Blender and 3D modeling so I’m having a hard to time explaining my problem. Im using Blender 2.47. Thanks for any help.