I'm using glTF Embedded files because I was told they are the best files to use with Godot, so I got a pack of a bunch of really lovely trees and other things to use in my game. But when I import it, it has all the materials on the side with the base being completely white. I know how to add textures onto things but it seems there is no way to add anything to the model? How would I use these materials then? Is this my fault or the model creator's fault?
This answer applies for the Godot 3 branch.
Open the model scene. Godot will ask if you want to open an inherited scene, or open anyway. Either works※.
Once you have it open, find the MeshIntance nodes in the scene tree. They have a material attribute where you can load or modify your materials.
Once you have it set up. Use Save as to save a copy of the scene as a new one. It is the new scene the one you will use.
※: What is the difference? The inherited scene will reference the original, and keep track of the modifications. Which is good if you are also doing 3D design and you want to work on it after it was imported in Godot, and have Godot re-import it automatically. The inherited scene also has the limitation that it will not let you remove anything. If you are not doing 3D design, I suggest to avoid that option. There have been discussion on changing this, since the way models are imported causes confusion to many users, which is why I specify this answer is for Godot 3.
If you are using Godot 3.2.4, you have the new fbx importer. It solves a lot of problems that Godot had with fbx in the past. I would still suggest gltf or glb because they are an open specification (fbx is a provative format), yet you won't have go out of your way if you want to import fbx into Godot, most of the time (some material attributes are not supported at the time of writing).