Using Atmel Studio with Arduino Starter Kit (Uno MCU)
There are many tutorials on programming Arduino boards (or any other AVR MCU) with Atmel Studio:

Creating new project:
https://asensar.com/blog/2013/how-to-setup-atmel-studio-for-arduino-development/

Configuring Avrdude for firmware upload:
https://asensar.com/blog/2013/how-to-integrate-avrdude-with-atmel-studio/
http://www.instructables.com/id/How-to-Load-Programs-to-an-Arduino-UNO-From-Atmel-/

Please see this post too:
Atmel studio 7 - my own libraries

Nothing to afraid of, just don't mess with lock fuses (relevant only if you decide to play with ISP programmer and arvdude/avrdudess). Use Arduino USB virtual COM port connection for firmware uploading, just like in Arduino IDE.

With Atmel Studio you don't have rich libraries available like in Arduino platform, instead you will have to program MCU, its peripherals (and other devices connected, if any) by directly accessing MCU registers. This requires some knowledge on MCU hardware (but it is a natural choice if you want to learn that). Eventually you can build your own wrapper libraries similar to one in Arduino.

Check Procyon AVR library too - much better choice than digging Arduino library sources (a bit old but still relevant, I always recommend it as a starting point for AVR library development:)
http://www.procyonengineering.com/embedded/avr/avrlib/