There is no real right way or wrong way with regards to the use of patch panels vs a hub.
On my network it's mixed. All of my users have drops to their desks. Some of their areas are sent to a switch is in turn is sent back to our NOC and wiredinto a patch panel, which then in turn goes inside another switch.
But then I have rooms that have nothing but large rows of systems (40 systems per row). Do I have patch panels there? No... And why, there is no need to. I just have everythingrunning directly into the switches that sit located in between the rows. The systems are not going to move, so why pay the cash to have everything run inside the walls for no reason.
Next look at a server room. Most of your servers I would think would not be going into patch panels. Normally they would be run directly into your switch. But you can also wire them into a patch panel.
What it really boils down to is
A: Is the needed connection permament to that location?
B. What is the aesthetics fatcor?
C. Physical location. (if you have to have a user connected that is 200 feet away, I would thrown in a drop by them, run the connection thru the walls, into a patch panel in the server room or directly into your switch/hub.