rupertz...
No, you aren’t really missing anything. The way EE works is completely different then what you are used to with pM. I think coming over from the pM side as you have (and I did) is somewhat of a disadvantage, you have to forget almost everything you know. At least for me, I had to re-read the manual a couple of times and then just play around with the initial install/templates to see what did what and how. Eventually the light bulb went off and I understood the EE system. Now that I know it, there is no going back to pM 
Good Luck…The effort will be worth it in the end.