Edit and complete your Disqus profile - Nobody wants to entertain a comment left by an anonymous person with no avatar and real name. Make sure your blog visitors do not face the same situation. The very first thing after installing this excellent system is to completely fill the profile details. This includes your real full name and a short biography about you.
An avatar is equally important to put the icing on the cake. You can also integrate external services like Facebook or Twitter with your Disqus profile to push your comments as tweets and posts on these platforms. Configuring notifications associated with your profile are also important and must be tweaked depending on the volume of comments you make and receive. Another important setting associated with your profile is the time zone that shows the correct relative time of your comment to the local users in different parts of the world.
Provide blacklisted words, if any - In some niches spammers are much more active compared to other less prominent or non-profitable niches. Although this comment system has a powerful spam filtering engine, but still if you think you're going to be bombarded by spammers, you can preemptively provide a list of well-known words used by spammers on regular basis. Make sure you separate each of these words with a comma. You can provide these restricted words in the 'Blacklists' tab. Power users can also use wildcard characters for these words.
Add moderators - This setting is very useful for blogs receiving large volume of comments on daily basis. Apart from the primary moderator (you), you can add unlimited number of supporting moderators to entertain visitors' queries. You can add these secondary moderators through 'Moderators' tab. You can also configure an important setting through this tab. Sometimes bloggers receiving massive number of comments disable them on posts older than 2 or 3 months. You can do the same here by providing the number of days after which comments will be disabled on each post.
Customize the appearance - By default, Disqus provides two custom themes for the users. But through custom CSS, you can completely customize the appearance of your comment threads. Here's an excellent post about customizing Disqus comment system. If you're comfortable with HTML and CSS, you can create a unique and visually appealing theme that integrates well with your blog's template. Make sure you always do this customization on a test install before transferring the custom CSS code to the actual blog account.
Enable Akismet for additional spam protection - Although Disqus has very effective spam filtering mechanism, you can further strengthen it by activating Akismet anti-spam engine. Go to Settings → Advanced → Akismet and provide the API key to integrate it with your Disqus account. This will give you a double layer of spam filtering system that will help in keeping your discussion threads free from spammers and bots. Once activated, Akismet system starts working immediately and provides a secure environment free from link droppers and spammers.
Import old WordPress native comments - Whenever we install and activate any 3rd party comment system on a WordPress blog, the old native comments stored in your WordPress database are no longer displayed on old posts. But you can pull all of these old comments into your Disqus database so that they can be displayed through your newly installed system. To import these comments, simply go to ''Tools -> Import' menu and follow the instructions. This process may take some time if the volume of old comments is extremely large.