Step 2. Once you download it, right click on it when it's on your desktop and choose to open it with java and it should look like this:
Then select Install client and press Ok and it should generate a new file in your versions file.
Step 3. If you didn't already have a mods folder in your .minecraft, there should be one now. If you alreadt have any mods in there take them out and put the Pixelmon file in.
Step 4. Change your Version to the one that says 1.6.2-Forge(Insert Version Here), when you have done that it should look like this:
After that click Save Profile and your done!