If you are having multiple websites using the same (one) database in Joomla, and wanted to use different DISQUS shortname (or account) for each site, it's very simple. Oh! This is for K2 DISQUS comment system.
Download 'Disqus for K2' plugin from here. Install this plugin to all your site.
In the plugin parameters write your 'shortname' for the main site as shown below.
For other sites you can hack the plugin code so that you can use different Disqus 'shortname'.
Go to plugins/k2/disqus_k2/ and download 'disqus_k2.php'. Open the file and go to Line 82. Below is the code you will see...
var disqus_shortname = \''.$pluginParams->get('shortname').'\';
Change this line as show below
var disqus_shortname = \'yourshortname\';