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I sorta understand and I sorta don't understand. But the answer to your directory question is "Yes". Instead of uploading your XOOPS version package files to public_html/main, you can upload the package to public_html
and install it there with no problems.
SiteMap issue: have you tried the XOOPS module for a sitemap?
You can pick up the SiteMap module 1.27a here:
SiteMap ModuleQuest