It is important to discuss this particular topic early on because it acts as a cog in the machinery of not only your site, but also in how your site interacts with the rest of the Internet. The simplicity of the Clean URLs in the SEARCH AND METADATA section of the Configuration overlay belies its importance.
As you can see, the choice is simple either enable or disable Clean URLs. Your system should also tell you whether or not it is possible to use clean URLs if you see something like the following screenshot, then you have problems:
It is critical for SEO purposes that you have Clean URLs enabled on the live site.