The folders section relates to where all your files are.

The map line is the folder on your computer where you have a site files. So for example you might have everything in

/Users/Adam/sites/domain.com

and then on Vagrant that relates to the directory

/home/vagrant/Code/domain.com

This is a shared folder and means that you can edit on your computer normally, but the changes get reflected in Vagrant too.

The sites section tells Vagrant where to find the files required for when you are viewing a site in a browser. In this case nginx needs to know to map

domain.com

to the files in

/home/vagrant/Code/domain.com/public

When you run "vagrant up" it will use this to tell nginx what to put in it's configuration.

Not sure if that will have helped or not :)