To get rid of the annoying focusing on the Agent's end every time a visitor sends a message all you need to do is add an extra condition to check if it's the client (or not in which case it's the agent) to the following in /webim/js/chat.js
if(!this.wt){window.focus();}
So it becomes:
if((!this.wt) && (window.location.href.indexOf('client') >= 0)){window.focus();}