I'll try to answer the questions...
I am working on the updated intro doc - there have been a number of recent changes in the product that will hopefully streamline things, and they're ready now, so that unblocks things. For a short while in the interim, you'll need to build the repository (which should be fairly simple). See the instructions at https://github.com/nikhilk/scriptsharp/wiki/Building,-Installing-and-Testing ... this is simply to pick up the latest and greatest which directly helps in step #4 below.
Once you have built and installed the resulting vsix (and set up a local nuget package source pointing to your local build)...
- Start with one of the project templates - eg. the jQuery App one.
- Any script# nuget packages and script# items go into the script# project (not web project)
- Add your code in there.
- Add your web project, and add a project-to-project reference from your web project to the script# project.
The generated scripts will be deployed into the Scripts folder within your web application automatically upon successful compilation.
I also recommend checking out the samples present in the github repository - you should be able to open any of the sample solutions in VS and check out how they're setup, the packages they use etc.
There is some good feedback between the lines of your questions. I'd love to see some of the pain points/confusion raised as issues, so they can be better tracked. Even better would be if you'd like to help improve the project over on github (https://github.com/nikhilk/scriptsharp).
Hope this helps, and thanks for the patience!