In Godot everything you can see and interact with is nodes. Each node can have 1 script attached to it. The nodes are organized in a tree graph (similar to how you would organize files in folders on a computer, except everything is both a file and a folder). Nodes contained under other nodes are its children. Nodes can have many children. Nodes can only have 1 parent. When a node moves, rotates or scales - its children do too. When it is deleted - its children are gone with it. You can also change the colour of the node and its children using modulate.
In a script it is usually quite reliable to look for a node that is your child and can be done with $node/path or by using an export (NodePath) var path_to_node; onready var node = get_node(path_to_node) (it wont be gone unless you are gone and is added into the world with you). It is less reliable to look for a node that is your sibling, dont do it using get nodes, use collisions/areas and signals where possible (it can be gone without an announcement). It is usually somewhat reliable to ask for your parent as there is always a parent (even if you are asking this in the top node of a loaded scene - there is always the root node), do it with get_parent().
If you want to make something a part of something - it should be its child (sprites + collision on a player, fancy animations on them, etc)
If you want things to independently interact - they should be siblings/under different parents so that they dont affect each other directly and instead do it through your intended channels (collisions, signals, etc)
Speaking about collisions. You might notice that each has a number of layers and masks. Collisions of layer 1 touch and can be touched by collisions with mask 1, but not other collisions of layer 1. If you want things to touch each other as normal - use both layer and mask. If you want players to hit walls but not each other - only use layers. If you want things that detect presence of players to not be triggered by each other - give them all masks so that they only react to players with only layers.