CentOS is an Operating System just like Windows is.
It has all the tools you currently use for a server like Apache, MySQL and PHP.
So after install (windows is gone) there's nothing you need to do, other then developing your website.
Then you will notice where and where not you may store files on the system thru PHP since the system is already protected.
After that we could guide you how to use encryption as used with:
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PHP: crypt - Manual
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PHP: md5 - Manual
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PHP: sha1 - Manual
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PHP: gnupg Functions - Manual
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PHP: hash Functions - Manual
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PHP: Mcrypt Encryption Functions - Manual
Windows is a mess if you want to properly setup a server with your scripts.
You need IIS knowledge since Apache will not provide the security on Windows.