The 
button is the most important button in the game, and the one you will use the most. Pressing Z will allow you to prepare a message to send to Pikachu, and releasing Z, will send the message.
The 
button, will let you pick up items and throw them, and advance through Prof. Oaks explanations. Note that you can not do this during Pikachu's Discovery Days, and when you do not have the Toolbox.
The 
button will bring up your PokeHelper, and open your toolbox.
The 
button gives you information about objects that the hand cursor points to.
Later in the game, the bottom and top C-buttons will make you switch between viewing modes. The bottom C button engages the 'View Mode' which allows you to look up and down using the control stick. The top C button puts you in 'Pikachu View Mode' which keeps you trained on Pikachu where ever it goes.