If the verification link in the email does not have the correct domain specified you would update this in the Globals file. In the Globals file this is controlled by this setting:
$WAGLOBAL_Root_URL
In the email that is sent the code looks like this:
<?php echo($WAGLOBAL_Root_URL); ?>users_Confirm.php?ID=
You just need to ensure that you have the domain for your site specified in this Global value.