When you have the key, hold it in your main hand and Season 3 Omnitrix in your off hand and click.
When Omnitrix times out (2.5 minutes), it enters the recharge mode, and takes 30 seconds to recharge. When an alien is chosen, right click and you will transform. Put the Omnitrix in your off hand and in the ninth slot you can sneak and change the alien shown on the Omnitrix.
The Omnitrix: Throw an emerald, a nether star and an iron block on the ground to get the Season 1 Omnitrix.