If you don't know how to compile via the command line I might question why you are managing your own server. Perhaps you should e-mail your data centre and see if they can do it for you, or hire a server admin company to handle it.
If you want the same as you have currently you'll need to copy the ./configure line from a phpinfo() file on your server. That will have all the correct paths etc. Then you can add --with-pdo and --with-pdo-mysql
You need to download a copy of PHP and then extract and run it from the extraction location. Also you missed a ' from the beginning of the --with-pdo-mysql. See the manual for instructions on compiling and installing.
It doesn't matter about the cPanel PHP build - your build will overwrite it when you run make install at the end of the setup process. Just follow the instructions as described in the PHP Manual for your OS.