On the first schematic PIN4 on the DIN connector looks like the labels are confused and the 5V one might be assigned to the ground connections.
+1. Clean it up! You will not be able to spot the problem with that rats nest.
First thing I would do is look up creating new components in your own project library. Then make a renamed copy of the ATMega328 component and move the pins from one side to the other so make the schematic clearer.
Like this for example:

Also... to change the values on the PCB you need to:
* Change the schematic.
* Export the netlist
* Import the netlist to the PCB layout - switch on "Allow change footprints" if you changed any.
Labelled connections do not need to connect. If you put a +5V on a point in the circuit, it will automagically be connected to any other point labelled +5V when you come to do the PCB.