1.) Double click the .exe file. It will create multiple temporary files, and make the directory a little bit messy, but that's nothing to be worried about. It'll clean up everything it makes.

2.) You will be prompted to select a texture pack folder. Select the folder of the texture pack, and enter "Y" to continue, or "N" to select a different texture pack folder.

3.) It will start spewing out data. This data tells whether the individual blocks from the texture pack have been done or not. (For example, look in "Screenshots" spoiler)

4.) Once the data has stopped printing in the command prompt, you are allowed to close the window.

5.) Open the texture pack folder that you selected earlier, and go into the folder named "textures."

6.) Delete all the textures that look like this
or

7.) Enjoy your updated texture pack!