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usually these are used in conjuction with each other to create AJAX pages. Basically you can create pages that have live elements. See AJAX

WHM/cPanel is the best out there. The next most popular is probably Plesk, it runs on both Linux and Windows servers. Lots of free ones out there too. These are the best paid control panels.

I like the logo, it matches well with the service you are offering. The website looks very professional and nice. I would really look at some of the grammar though as others have stated. Once that is worked through it will be a great site.

the .htaccess file tells the apache web server to do various things, like redirects, etc. If you are using cpanel for your control panel then use the File Manager and just create a new file in the root of your public_html named .htaccess Then you can edit it with whatever requirements you need.

You should use google analytics or another analytic program that can tell you where the traffic came from. This would give you what you are looking for.

If you mean someone hacked or found a script on your site, then it is probably because these are both open source. Meaning, the code for all of wordpress and joomla are free to look at. So basically all core wordpress sites are exactly the same, with the same structure etc.