How to install Centos 6.4 by pendrive with windows dual booting in two separate hard drives ?

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I can't talk from experience because I have never done this per se. I think you think you have two options.

  1. Would be to repartion your existing windows machine to free up some space for you centos system. However, this is always frought with danger. You could loose all your existing work.

  2. Far safer is to back up all your windows important files, programs and documents onto an external harddrive. Format your system using the windows disc and whilst there create two partitions one for windows the other for centos. Install windows on the primary partition then install centos on the other partition.

1.Install the Unetbootin software on your system from this link and then save the iso image of the installed centos 6.4 in the pendrive.
2. Install the centos 6.4 from the pendrive by following the dialogue box instructions.

Honestly, I do not recommend dual-booting operating systems. I have found it to be prone to serious problems. Myself, I use a virtual machine manager, such as VirtualBox, to create multiple virtual machines, with their own virtual HD wherever I want it. It preserves the fabled KISS principal. -)

FWIW, Sirajhyd's suggestion about Unetbootin works here as well!

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