You should read most of the articles on this page before you decide to proceed:
Compatible Products – Arduino Help Center
There are legal issues that you should consider.
But to make a PCB with all of your stuff on it you can start by learning KiCAD:
KiCad EDA - Schematic Capture & PCB Design Software
I'm just learning it myself.
You'll also need to understand the Uno's schematic:
arduino_Uno_ref.sch