The poke ball has nearly as many mysteries as the pokemon do. After the recent episode with a Josh Waterflower, there have been many things revealed. In addition to capturing pokemon, it can also transform humans into pokemon. There are a few rules that go along with it.
First, if the person is unaware, he or she will be able to choose for themselves what to turn into. If the two persons involved have agreed to fight and one loses, then the thrower will chose.
Second, the victim will have one year to make him (her) self revert to human form. They may revert by being captured again within that time period. However, people will know that (s)he has been human because the speech does not change. If they do not change back into human form, they are the equivalent of wild pokemon.
One more thing, a person can give themselves up to a human, as a sign of loyalty. If they were changed against their will, then they have the option to slip back into their original form. If they have agreed to turn into a pokemon, then they cannot redeem themselves.
Third, your pokemon will be allowed to go to whom you please.