Why are there 3 crystals on the Mega2560 schematic? I am a software engineer who is new(er) to electronics, I only started a couple of months ago. I've built a bunch of custom circuits, then some arduino nodes that are around my apartment that communicate with a C# server. So I've at least got the breadboarding part down.

So now I am working on a controller board that connects to my home automation system and determines the color on the LED light strips I installed into my bookshelf. So I want to transfer from working with pre-built Arduinos to building my own full node, there are some things I think I'm missing. 

I've noticed that there are duplicate parts on the schematic for the Arduino Mega2560 schematic (such as there being 2 voltage regulators - one is replacement if the other is not available). I couldn't find any such description however for why there are 3 crystals located on the board. I see 3 different circuits for crystals (all of which are 16MHz).

Specifically, I am referencing the following
One of the crystals is for the ATMega8U2 chip which is being used for USB-Serial conversion.

The other two crystals are both for the ATMega2560. Why two? Basically they only populate one of the two, but they have two different footprints. One is for a surface mount resonator, the other for a through-hole crystal. 

Having two footprints gives the option during assembly to go for the cheapest package at the time. It also means that the hobbyist can replaces the low accuracy resonator with a high accuracy crystal if their project requires. 



As a side note, if you look at Y1, you will notice it is not the symbol for a crystal, it is of a resonator.