I think you may be hehe
I haven't tried it personally, but from what i understand, wherever you set your "store_into" to be, any sub-dirs from there would be included. Anything of a higher-level (ie. dirs below) won't be.
Of the options you can either modify or delete, this is how I understand them:
URL - Include urls here that wouldn't otherwise get picked up (ie. maybe other subdomains in diff folders). If you dont have urls outside, you can prob delete this section
URL list - if you have some file of URLs alreday, otherwise you can prob delete this section
Directory Paths - if you have paths you want included that are on the filesystem outside the DocumentRoot (or in this case the store_into I guess). If you dont have such case, delete this section
Access Logs - I'd use this one, esp. if you have any dynamic pages. Any URL found in the logs would then be added to the sitemap. Could make your map huge though if you have very dynamic pages and tons of urls, not sure if that might cause problems or not.
Sitemap - include other sitemaps you've already generated. Not your case here so just delete that section.
That's how I understand it, hope that helps some
