Okay, I'll give you a short tutorial on how to use Poke Transfer.
First, you have to choose the one to six Pokemon in your Gen IV game's box to transfer. These Pokemon are put into a bit of a mini-game, in which you catch these Pokemon using a Pokeball... Crossbow, of sorts. Basically, the device shoots Pokeballs at the Pokemon to catch them. In order to fire the Pokeball, you pull the Pokeball back using the stylus, then release. The Ball will fire at the spot you designated. Don't worry, there's no limit to how many Pokeballs you can use.
Pokemon hide in the tall grass in Poke Transfer as well, and throwing a Pokeball in that patch will make the Pokemon in that patch scatter. This is your chance to catch those Pokemon by throwing a Pokeball at them. Like in Pal Park, capture is guaranteed. Once all Pokemon are caught or the timer reaches zero, the game ends and you are given an option to bring the Pokemon you caught or not. In either case, Pokemon you failed to bring with you stay in your Gen IV game's box.
The instructions for starting up Poke Transfer are explained in-game.