It is not so complicated. Let say you have an RF receiver. You design an front end amplifier, that has 5 or 10 parts to it. You test it, optimize it, and put the design info into folder #1. You then design a downconverter block with some parts in it, optimize it and put the design info into folder #2. You then design an IF section, where you design an IF amp, a Variable gain amp, and some sort of filter, test it, and put the design info into folder #3. You design a switching voltage regulator, test it, and put that into folder #4. You design a local oscillator, test it, put the info into folder #5...and on and on. At the end you give all the folders to the board layout guy, and he makes a big printed wiring board with all of the stuff on it. You work with him to add some mechanical items, like metal shields and connectors. He finishes his layout, and you look it over to see if there are any RF problems he has introduced.
You then fabricate the board, assemble the parts, test it, and hopefully it works.