Flash Arduino Micro code on Atmega32U micro controller First of all, I am not an expert on electronics, so forgive me for asking something which is trivial for probably the most of you.

I am trying to get my Arduino (Micro) code running on a custom PCB with the Atmega32U chip on it. The person who made the PCB copied parts of the schematics of the Arduino Micro onto a custom PCB. What he did, is place the Atmega chip on it, and also copied the wiring for the micro USB connector.

That way, I can hook up the PCB to my USB port but now Windows does not recognize the chip as a "Arduino hosted via a COM port", but just as a atmega chip.

I learned that installing Atmel Studio 7 will also provide the correct drivers so that Windows recognizes the chip correctly via USB: 



The next step for me was to get my code running on the atmega chip. So with some help from the internet I came to the following steps:


open my sketch in Arduino IDE
compile with verbose output
find the location where the ".HEX" file is stored


But how can I flash this .HEX to the Atmega chip?
To get your chip to respond to the Arduino environment over USB you need a booloader (some extra code) to be running on the Atmega32. 

To install the bootloader you can use another Arduino as a programmer to the ICSP pins (or any other AVR ICSP programmer).
This procedure and description from Sparkfun for the Arduino Pro will help you.   

This may help you understand the ICSP aspect, again from Sparkfun.