I suggest that you have a look to the tutorial video 0.d that give you an overview of different possibilities.
1) See also tutorial video CP-05 that show how to create slave site with specific /images and /templates directory. You also have tutorial video 0.b slide 31-34 that show different possibilities.
Full sharing, Full copy and partial sharing of the /templates directory.
2) If this is a domain and that you are using cPanel, go in cPanel addOn and create the domain using a specific document root.
Get inspired of the directory structure that you can find in tutorial video 0.b slide 21-24
In general we recommend a directory structure like "domains/yourdomin.com/public_html"
3) This is a good practice to preserve the master and replicate it into a specific place.
When I am doing a configuration for the customer, this is what I am trying to do when this is possible and later I rebuild a slave into another DB that become the original website.
So you could move your existing website in master.yourdomain.com and later create a slave that restore the
www.yourdomain.com