Having an empire makes things easier when you grow beyond a certain size. For example, in one of my unfinished games as Francia, I have around 1200 holdings under me. Having everything under one Empire makes it easier to manage. I still avoid making "Kings" other than to expand (e.g. count title to a pretender of Poland, then conquer Poland and make him King, then later make him revoke his title by making him revolt/etc). King titles to vassals can make dealing with Dukes easier as 100s of Dukes are a pain to deal with, but King tier vassals are dangerous especially if they revolt when you are away.
Finally, it is useful to make King tier titles when you expand outside of your de jure area. Dukes are less likely to rebel if you are the de jure King of the Kingdom and also their emperor. Similarly, Kings are less likely to rebel if their Kingdom is in your de jure empire. Making these Kingdoms is often worth the opinion hit of not handing out the Kingdom (-20 to every duke that wants it) because there is a hidden rebellion modifier (15% I believe) when you are not the de jure liege of your vassal.
As far as de jure titles go, as long as the duchies are in the Kingdom, they are less likely to rebel. As long as the Kingdom is in the Empire, the Kings are less likely to rebel. There is no need to make the Dukes part of your de jure Empire as long as you are their King as well and the duchy is in your de jure Kingdom. Don't hand out the Kingdom to any vassal till the Kingdom is in your de jure empire (or if you play like me, don't hand out King titles other than on very rare situations).