For my website, i want the user to confirm his email address(by clicking on the email-activation link in his/her mail) and only then be allowed to log in to his user account. This happens perfectly well when a user's password is generated by drupal. But i want this to happen after using LogginToBoggan where user sets his own password. How do i do it?
You may take a look at this module http://drupal.org/project/logintoboggan_prevent
Unfortunately, it has not been ported to Drupal 7 yet...