As you progress, you'll want to start using JP->JP dictionaries like http://weblio.jp and http://goo.ne.jp. You'll need them when you encounter words not included in any JP->EN dictionaries, anyway.
As far as reading VNs goes, I'd recommend using a text hooker and pasting the text into your browser, then using Rikaichan to look up the words you don't know. In any case, avoid using machine translations.
In terms of learning, the most important thing is grammar. Looking up words is usually easy, figuring out unfamiliar grammar often is not.
And as has already been said, forget about learning readings without the accompanying meaning.