* http://makezine.com/projects/make-36-boards/make-your-own-dm...
* https://learn.sparkfun.com/tutorials/using-eagle-schematic
* https://learn.adafruit.com/boarduino-kits/overview
It's also good to know the lower level concepts of directly programming an AVR:
* http://hackaday.com/2010/10/23/avr-programming-introduction/
https://learn.sparkfun.com/start_a_project
I find some of the articles on PCB Design magazine to be useful for PCB layout.
http://design.iconnect007.com/
Note that a lot of hobbyists use 'Eagle' which is free(ish) as in beer. Profession tools are $$$, though Altium offers http://circuitmaker.com/ (which I can not speak for).
Basic: https://www.amazon.com/Getting-Started-Electronics-Forrest-M...
Intermediate (with a heavy RF slant): http://www.arrl.org/arrl-handbook-2015
Advanced: https://www.amazon.com/High-Speed-Digital-Design-Handbook/dp...
And then there are the various subcategories: low level precision analog, high power motors and switchgear, basic digital and microcontrollers, high speed processors, etc... you're asking a wide open question.
Even Manufacturing is not a simple question to answer unless given some direction. You want to make a first PC board in your bathroom, or build complex electromechanical assemblies?
I don't know if any single tutorial is going to give you what you want. I'd just dive right in, figure out what you want to do with your board, select some parts at Digikey, and start designing. Google questions as they come up.