It is very easy to optimise your site database within iControlWP.

To perform database optimisation for each site, select to manage the site from the sites listing view, choose the "Optimise" tab, and then click on the "Analyse Database" button:

Once the database has been analysed, you will be able to see what should be optimised and then you can perform the optimisation if you want:

For more information on how to optimise your database, read the blog article here.