First, learn vanilla JavaScript. Don't bother with all those libraries and frameworks as they try really hard to iron out JavaScript's particularities. When you know how to deal with scope, the prototype chain and a reasonable amount of DOM stuff you can choose tools to make your life simpler or realize that all the snippets you have accumulated are, in fact, your own framework.
Two, forget your traditional OOP roots, JavaScript is loosely typed, it doesn't have classes… it's very different. You simply won't be able to use it like Java.
Three, Eclipse (and probably other IDEs, too) is perfectly capable of debugging your JavaScript without using `window.alert();`. When testing your code in the browser you can use its own dev tools to inspect values at breakpoints and so on. Webkit's dev tools are my favorite.
Four, install a CLI interpreter with a REPL if you don't have one already. `jsc` is standard on Mac OS X but there are a lot to choose from, including `rhino`, `spidermonkey`… Your browser's dev tools has a REPL, too, if you like it more. Either way, a REPL is very handy when you need to try out a few things without messing anything.
Five, you might want to force your code to comply with loosely defined and not even widely accepted code standards. Installing a `jslint` variant on your system may help.
Six, keep in mind that JavaScript's development is definetely not centralized. While there is a standard body officially responsible for its elaboration, nothing is written in stone. New frameworks/ideas are poping every week only to be replaced by a "better" alternative the week after. It's all vey exciting but also very chaotic. Focusing on the basics first will help you keep your head above the water.