How to send two different email with different bodies using phpmailer ?

All you need to do is call the send_mail function twice. Something like:

require 'PHPMailerAutoload.php';

$mail = new PHPMailer();
/*Set Mail settings for first email */

$mail->send();

$mail = new PHPMailer(); //We reset the $mail variable to a new instance of the class
/*Set Mail settings for second email */

$mail->send();

By doing this you essentially reset the class and can send the second email. You can also declare a second instance of the class by changing the variable in the second instance.

It my not be the best way to do it, but I dont see why you couldn't initialize two PHPmailer objects with a form submit. The first PHPmailer object could email you with the message details, the second mailer object shoots an email to whoever submitted the form. I didn't see anything in the docs that allowed this to happen within just one mailer object, but I only took a few minutes to glance over it all. But...

From a pure user experience point of view, if I submit your form, clouding up my email box with a email that only says something like "Thank you, your message was received, well be in touch shortly" is poor user experience. Don't take up my time by making me organize or delete this random email in my box. If that is the case, a simple confirmation on screen is more than enough for me to know the message went through.

The only time I think it's okay to send an email after a contact form submit is when the email contains information just for me; such as maybe a reference or ticket number when I'm inquiring about technical help; or emailing me a receipt if the form is a purchase. If you're going to send me an email, make sure it contains information somewhat private or personal.

Just ask yourself what benefit is the form submitter getting from your email. Thats all :)