Could you go over how layers work? That is one thing I would like to know more about.
Lucky for you, I already did! Check out MTG Tutorials #27 Part One: What is the Layer System? and Part Two: The 8th Layer and Beyond.

seen from Brazil
seen from Brazil

seen from United States
seen from United States
seen from China
seen from United States
seen from United States
seen from United States

seen from France
seen from United States

seen from United States
seen from United States
seen from United States
seen from Yemen

seen from China

seen from United States
seen from United States

seen from Ecuador
seen from Malaysia

seen from United Kingdom
Could you go over how layers work? That is one thing I would like to know more about.
Lucky for you, I already did! Check out MTG Tutorials #27 Part One: What is the Layer System? and Part Two: The 8th Layer and Beyond.
I'm slightly confused about the Layer System. Say I have a Tree of Redemption in play and I activate its ability. Then, I somehow put a copy of the Tree into play. Does it come into play with 13 toughness since the copy layer comes first? How is this different from your past example with copying the Clone when Humility is in play? Thanks in advance.
The Layer System is only used to reconcile continuous effects, that is, effects which are passively ongoing and affecting an object at a given moment.
If you’re talking about responding to Tree of Redemption’s ability, creating a copy of the Tree before the ability resolves and the Tree’s toughness changes, then yes, the copy will be 0/13, because that’s what the original Tree looks like at the moment the copy is created.
On the other hand, if you’re creating the copy after the Tree’s toughness has been changed (to 20, say) then the Tree copy will have the new value for its toughness.
Remember -- copies are almost never linked to what they're a copy of once they become a copy. After that point the two objects exist independently from one another and modifying one will not change the other.