Well in a nut shell, Cpanel is just the Administration side of your webhosting account.
Hostgator like many other providers give you your own php.ini they also allow you to make certain chanes to httpd.conf.
It will take you awhile to start using CpanelX to it's full potential that's even if you ever do.
The best way to make use of it, and seriously is if it's not broke don't fix it.
Usually people upload their files and alter these settings to the requirments of their software they have uploaded.
A good place to get started is using Fantastico to install scripts and portals such as joomla and wordpress.
If you need any further help give me a shout on msn or email me.
<email snip for spam protection> i would be glad to help =]
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