Instructions
Travel to a Pokemon Center located in any city or town. You can also enter your Secret Base or bedroom in New Bark Town.
Walk to the PC and press "A" to turn it on. Select "Someone's PC" to access the Pokemon storage system. If you have already met Bill, Johto's PC developer, select "Bill's PC" instead.
Select the box number you would like to deposit your Pokemon into by pressing the left and right directional keys at the top of the screen.
Select "Deposit" and choose the Pokemon you would like to put in the storage box. Your Pokemon will be taken from your party and deposited into the PC box.