Some general advice is to install and use SuExec and SuPHP on your server. You can do this by going to WHM -> Software -> EasyApache. Go through to step 5 then check the box for SuPHP. Sit through the compile process then at the end you will be prompted for how PHP should be run - select SuPHP.
Also review items in WHM's Security section, especially Security Center, to determine which security measures are appropriate for you to implement on your server without excessively inconveniencing legitimate customers.
Regarding how many people have downloaded a specific file, just view your website stats in cPanel (Analog, AWStats or Webalizer). Stats are updated every 24 hours by default.
I'll move this thread to the WHM questions section so you may receive more relevant responses from other forum members.
Details? These forums are full of details on how to secure your server. Use the Search function.
Mike
If you do not have access to WHM, these questions are best addressed by your hosting company rather than these forums. These forums are for folks who run their own cPanel/WHM servers.
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