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It's quite simple, actually. If you go to the Pokemon center and look at Nurse Joy's desk, on the far right side of the desk is the PC box. Go up to it, tap A, press DEPOSIT POKEMON and drag your Pokemon into the PC box. Also, if you have 6 Pokemon in your party, any caught Pokemon will be sent to the PC box.
the PC is located in the large red buildings known as Pokemon centres. They are located in each town or city that you pass.

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