Yes this ought tot be explained better - also why it is better to it the Pi-way for new users
Have a look at the pi-top blog menu option on this site. There are several tutorials of using the proto board which might be sufficient to get you started.
If I removed the GPIO headers, I would have to use a Micro USB to power the Pi?
Can I use the USB Header next to the HDMI port?
What is the 4 pins on the top of the HUB for?
There seems to be, for what ever reason, NO-DOCUMENTATION! The answer is to unplug the 40 pin connector from the pi and using a continuity tester figure out which of those 40 pins are connected to the connector under the power/video board. When you do that, please publish here.
That is what I will do unless someone does it first.
The pins of the connector under the hub-controller have been published several times in this forum. See the attachement