This tool is meant to give you a chance to play the game without having to print it. The Event and Victory piles in this tool function in exactly the same way as two normal printed card piles would.
These are the large two buttons in the middle of the tool. Clicking on either of them will result in a card being drawn. You can check which cards have been drawn on the text output field.
There are several Pokémon buttons present on the tool. These buttons represent the Pokémon abilities that change the way you draw cards from the piles. From left to right, the buttons represent Natu, Xatu, Articuno, Mr. Fuji's House, Umbreon, Espeon, Marill and Jynx.
When you decide to use Natu's, Xatu's or Jynx' ability to choose one of the 2 or 4 top cards of the event pile, click on their button. 2 or 4 cards will now appear on the screen, and you will have to click on the one you want. After you click on one of the cards, the tool will draw that card.
When you decide to use Articuno's ability, click on its button. Two cards will be drawn from the Event pile. When you are done executing (or discarding) the cards, press the Done button.
When you land on Mr. Fuji's House, click on its button. Two cards will be drawn from the Event pile. When you are done executing the cards, press the Done button.
When you have an Umbreon, you may always look at the top card of the Victory pile without drawing it. To do so, just click on the Umbreon button. When you are done, press the Done button.
When you have an Espeon or a Marill, you may always look at the top card of the Event pile without drawing it. To do so, just click on its button. When you are done looking, press the Done button.
There are a few other buttons present on the tool, namely the Done, Undo, New Game and Help buttons.
The Done button can only be clicked when you are busy doing something. When you press the Done button, the tool will finish the current action and return to its normal state.
The Undo button can reverse an action like accidentally clicking on a button that draws a card. You can undo as far back as you like, but make sure to not confuse yourself when doing so!
The New Game button will reset everything, allowing you to start a new game. Don't worry, a confirmation window will open when clicking on this button, so you won't accidentally reset your game.
The Help button simply leads you to this webpage.
If you have any questions related to this tool, please ask them on the forums. This tool is also useful for people who are too lazy to shuffle the piles before starting a game, or for people who suck at shuffling.