As an arduino noob, it wasn't clear to me why you need a resonator component, especially since it isn't present in your first schematic?
Also, have you given thought to what happens after the battery runs out? Can the battery be replaced by the customer or does the device need to be disposed of?
The resonator is shown in the 'Eagle schematic', right in the middle of the picture. The first schematic is just for the moisture sensor. I used it as a crystal to run the ATMEGA.
When the battery is gone, you just pop open the enclosure and put in a new CR2032 coin cell battery. You can get those at every gas station or supermarket.
So an ATMEGA uC needs an external oscillator to run? Is it to provide the clock signal or for something else? If so, why doesn't it have its own clock signal generator? Wouldn't it always need one to run at all?