Is there anyway in sitemapper to just display the subcategories and not the root categories in the sitemap?

You can exclude files and or folders in the options area.

Scott, I'd like it to just show the subcategory, not the main category...If I ignore the main category in sitemapper the subcategory gets ignored also...

I attached a screenshot of how my sitemap html output looks...

Ah, I see what you are saying now. No you cannot do that with the software. Sorry.