When SEF-urls are made automatically it includes the category like mydomain.com/category/title. Can I change this so that it only uses title or title alias ie. mydomain.com/title ?? (I can of course make it as a costom url, but would like this to be something that could be done automatically) Is there any difference between paid version and free version in this respect?

You can adjust this in JoomSEF / Manage Extensions / Content where you can set what should be part of the URL.