Our goal is obviously to not be confusing when it comes to this stuff. I would recommend keeping a single thread for your issues open. Posting the same thing several times will just add to the support queue and will likely lead to even more confusion if multiple support people are all working on your same issues without realizing it.
One thing I can recommend right off the top is to just play around with extension and see what you can figure out that way. The help is definitely there to aid you, but in some cases just trying the product first will get you going.
You add a new site type in the main quick insert UI. When you select a site type, click the define button, change whatever you want and click OK. It will prompt you to save a custom site type.
With this product I would recommend using the main quick insert first and learn about that. Then worry about the preset manager. It will be easier for you to understand that way.
As for your template issues, it looks like you already have some support going there. We have done many tests with custom DW templates and have used those in Site Sculptor fine. As with any user defined file, its always possible there is a variable in there that could be causing an issue, but its hard to anticipate every single variance in a template someone might use.
The 18 site designs are starting points, but you can use DW templates or CSS Sculptor presets to create your own. You can also theme (change colors and images) any of the existing 18 designs and save custom themes. That gives you a lot of flexibility in terms of look and feel even for the stock site designs.