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Andrwski:
The only thing that would be, maybe, dumb, would be to keep those questions to yourself. Asking is the way to learn, and learning is the way to mastering your XOOPS site, so go ahead.
Yes, you can delete all the themes you don't want to use. You can also delete, from the particular modules' folders, all the language folders you won't be supporting in your site.
To set up the order of comments in your site, go to Admin > Preferences > General Settings. There you'll see a selector with the label "Default Comment Display Mode". Change it to flat and save the page.
Cheers.