On this page you will find a quick-and-dirty "getting started" guide. For more information, see this relatively complete translation of the manual.
If it starts with an intro, click the "X" (とじる） to cancel it.
At the main screen, you have two squares to write the words in. It doesn't matter which one you start with; the reason you have two is so that you can write in one while it recognizes what you wrote in the other one (it takes a few seconds to recognize).
You must generally use the correct stroke order if you write kanji. But, when it recognizes it, it will put it in the little black box in the middle of the screen. If it's wrong, don't delete it (with the back arrow button); instead, try clicking on it. It will show you the nine most likely alternates you might have written.
Now, to get Japanese definitions, along the lefthand screen, you will see four icons. The one you want is 和英（わえい、Japanese<->English). This way all of the definitions will appear in English. But, if you want English to Japanese, click the one above it, 英和（えいわ）.
Then just click the words you want. To save links to definitions for later, click the button next to the little letter A at the top. 登録（とうろく, records). If you click the A, it will give you B, then C. These are 3 lists that can store up to 100 words each. It's good to save every word you might need later that you look up on the go, and then you can study them some other time. To get your lists of words, click the tool in the bottom left corner, then choose しおり. You will see a history of what you've lookd up plus the A-B-C lists along the bottom. You can also erase lists from here. But it's very stupid, so you have to erase the whole list (all of A, or all of B, or all of C), not just a few items. So be careful.
If you see a blue link in the text you can select it by choosing ジャンプ (jump), which is in the middle of the top of the screen (also blue).
This should be enough to get you started. Oh, you can also use L+R triggers to cycle through what you've looked up.