I'm not convinced that IETester changes the underlying APIs correctly. Because of bad experience with "Multiple IE" simulators in the past I don't test on anything but the real install.
Yeah, I had trouble with those "portable IE6" implementations too. But IETester seems to be a lot closer to the real thing, at least as far as I can tell.
IEs4Linux might work for you then. It can install the original IE6, IE5.5, and IE5 under Wine. IIRC it uses a separate wine tree for each version, so there's no chance of the IE6 js interpreter being run in IE5.
You need JavaScript, and though there are lots of libraries that make things simpler, you'll need a good understanding of JavaScript and preferably have a good understanding of the DOM as well.
Libraries will help you with the DOM, but not a ton. They won't help you with the js.
I suggest you start with a library, but make sure you understan what you're doing in terms of the DOM.
I had a chance to chat with them - I honestly think lunascript and its platform is the core product. The productivity app they're building is a first show case (and in-house infrastructure)