What fold do I upload my index.htm file to? So that when you type in xtrememayhem.naget.com it appears? Would it be
/var/www/html?

If not which one?
And also where would I upload my .php files to?

Thanks for anyhelp!

yes, that looks like the correct folder to upload to.
php files may be uploaded to any folder you wish. perl scripts usually must be in the cgibin, php scripts can be anywhere.