-Image edition program (photoshop is your prime choice)
Additionally animation/video editing program if you want to animate elements, and audio editing program if you are gonna make your own soundfont
Take a look at other skins for inspiration. When you make a skin, make sure to have a theme so it's consistent
Take a look at the skinning wiki so you can see all the elements to skin, and every skin.ini parameters
The difference between @2x and nothing is that @2x is twice the resolution of the normal resolution, it's HD elements, so you might want to skin @2x elements first. There's an image scaler program to scale them down to SD resolution on skinship.xyz, in it's resources.
Watch some YouTube tutorials to learn whatever you need