What ebook reader are you using?
Opie-Reader has a number of ways to select words and text and copy them to the clipboard. Then just open the translator and it should just grab the clipboard and translate it. If it comes up in Japanese then you need to change the settings from EN -> JP to JP -> EN.
The dictionary has a psaste function that should allow you to lookup Japanese words, I'm not familiar with the C3K inbuilt dictionary, but the Cxx0 and C1K dictionary has different tabs for each of the dictionaries, switch through the tabs till you get to the JP -> EN one and your word with tranlsation should be there.
Stu