First, you need the seal case and some seals. Go to any PC, and boot it up. Go down to Your PC and select it. Choose the "Ball Capsule" option. Choose a Capsule and hit edit. Put the seals you want via touch screen. Drag it on to the capsule. Push the button on the bottom left of the screen to test it. When you are finished, hit confirm. Now choose the capsule you edited. Hit set, and choose Pokemon you want to equip it to. You can change the order of the capsules in your box by choosing a capsule, and select shift and choose another capsule.
Keep in mind that:
*You can only have up to 8 seals per capsule.
*It does matter where you put the seal on in the Capsule.
*To remove a capsule from a Pokemon, simply choose the seal and hit remove.
*You only need 96 of every seal because you can only have 8 seals per capsule and you have 12 Capsules total.
For more info on seals, go to the seal guide at: