I was board and decided to connect my Arduino Pro Mini (3.3v) and my AtomRTC along with my breadboard buddy pro on my breadboard. I can program the arduino using my breadboard buddy pro, which now communicated with my AtomRTC. So i get a nice UART console with the time/date info. I recommend this tutorial. Even tho its for the Sparkfun RTC (mines is the same almost) just follow the pinout of what ever board you use.
Here is my ugly picture 🙂 Feels good !