To use JavaScript to write a Windows 8 app, you should choose the JavaScript template in Visual Studio. Make sure you choose the one destined for the Windows Store. You need to consider that there are different states that you app can be in. I personally use Visual Studio to develop apps. You could also use a product called Blend. I hear it is good for layout.
You must delcare what capabilities your app needs to access. This info goes into your manifest. Be warned that the default manifest for Visual Studio app projects has Internet Access checked. Your app will get failed if you leave this checked and do not provide a privacy policy for your app. If you app does not require Internet Access, disable this capability!
Active X control are not allowed in your apps. Plug-ins are also not aupported. File access is blocked. Windows alerts do not work. You also need some tricks to access innerHTML as well. The Windows prompt is unavailable.
