What to you mean by "how [it] works"? Are you asking for the Exchange internals - how it is architected, what algorithms it uses, etc? Or are you asking from a user perspective - how to set up Exchange, how to attach email clients to it?
Also, considering your reference to gmail and yahoo, are you perhaps referring to Microsoft's Exchange offering within the Azure cloud?
The thing I wish to ask you is , what is the exact difference between the IMAP/POP3 and Exchange servers.
I am not asking it as a user perspective , instead you can tell me why this Exchange server is developed ? What are the different features of exchange servers ? Why and where to use it ?
IMAP/POP3 are standards (standards that Exchange implements). Exchange, like many email server, offer capabilities above and beyond those defined by this these standards. The best place to learn about these extra capabilities is in the Exchange documentation, which you will find on MSDN.