Conflicts of index.php files

[comppro1]

https://www.xml-sitemaps.com/ maps the first 500 links of my large site.
My host puts add-on domains in sub folders of the first domain, and I
have index.php in the top, several add-ons, several sub folders.

documentation.html for the $20 stand alone version says to install in
the folder I want mapped. The install includes index.php which is
in conflict with the existing files. What should I do?

Why can't I set up outside the domain to map, like [ External links are visible to forum administrators only ]?

My top domain contains two folders for /store and /blog that I'd like
to map separately. Both have index.php.

Intial config.inc.php includes
'xs_initurl' => '[ External links are visible to forum administrators only ]
'xs_smname' => '/usr/home/public_html/sitemap.xml',
'xs_smurl' => '[ External links are visible to forum administrators only ]
Why is 'xs_initurl' at the top, not the sub folder to be mapped?

[XML-Sitemaps Support]

Hello,

you should create a separate folder for sitemap generator script inside your domain folder, like:
www.domain.com/generator/ (or any other folder name)
and put script files in that subfolder (including index.php etc)