Learning embedded systems design with microcontrollers will teach you how to design a board and bring it up. Try http://www.avrfreaks.net/ for some projects with Atmel AVRs. There's also http://www.sixca.com/, http://www.eevblog.com/, and http://www.webring.org/hub/avr
Really, your question is quite broad and there are many ways to approach learning these things, but this is the direction I came from originally and it has worked well for me.