Can somebody please explain to me the relationship between:

1. Account -> root directory and
2. Project -> Top publishing directory

thanks

The important thing is that when you put the account root directory and the project top publishing directory together, they should form a valid path.

Here is an example of how I typically set it up:
1. Account -> root directory: /home/username/public_html
2. Project -> Top publishing directory: /

The above uploads files to the /home/username/public_html/public_html directory.

The following will work equally well:
1. Account -> root directory: /home/username
2. Project -> Top publishing directory: public_html/