To get started with programming, especially with JavaScript, I think this is a wonderful place to begin your journey: http://www.codecademy.com/ It uses JavaScript for the very basic beginner course, too. You get medals and all that, and it's well implemented. :)
After this, look up "Eloquent JavaScript". There is both a printed book and a free online version. It's very in-depth, but not too dry as far as IT books go. The HTML5 book in the "Head First" series also covers JavaScript, but since you want to learn programming from the bottom up, Eloquent Javascript is a better choice, after the Codecademy.
I don't think you need an IDE yet, but the best one I found for JavaScript is Jetbrain's WebStorm (costs around ?45). A free alternative would be Netbeans. But as I said, I really don't think you're at that point yet.