Minecraft wiki entry for Updating_old_terrain, associated text: MCEdit has three camera modes. A sideways camera that looks like Terraria, an overview camera that shows the world from the top, as well as a full 3-D camera. You can switch between them using the three buttons labeled 2D, Over, and 3D. For this tutorial, we'll be using the overview camera.
Press and hold the right mouse button to move around.
The toolbar is on the left-hand side of the window. For this tutorial, we'll only be using the Select tool.
Using the chunk selector, you can select chunks by dragging a box with the left mouse button.
The status bar at the bottom of the window shows a lot of useful information about whatever you're pointing at with your mouse cursor. In particular, it shows the block coordinates, chunk coordinates, and the biome. You will be using the chunk coordinates to define protected regions.