Substance for creating an atlas

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Krato polygon
First off, I am a noob with this stuff. I've learned a lot in the past month and I have a lot (seemingly endless amount) left to learn. Please forgive me if these questions come off as dumb. I have learned a lot about modeling, but over the past week I have been venturing into the texturing process and It's still quite mysterious...

 
I received some good advice from the community the other day regarding approaches to texturing and I've been trying to figure out how to efficiently implement their atlas suggestions. I want to experiment with creating an atlas having textures for wood, metal, and whatever else. I have been watching the allegorithmic "creating a texture atlas" tutorials. While they are helpful, I'm not sure if it's the right step for me yet; more on this soon.

 In terms of texturing, I have been playing around with substance painter the past two weeks and learning a lot about that process. Moving on to Substance B2M3, I took an image from online, imported it into B2M3, and followed along with a tutorial. I now have a wood texture that I'm satisfied with that works in Unity. However, at this time the wood material takes up the entire space in my 2048x2048 supposed-to-be-atlas texture map. 

The question that I'm now wondering about is: Is there a way for me to take this B2M3 created wood material into substance designer and set it up so it is formatted like they have the materials in their atlas tutorial? I ask because in the atlas tutorial they use "PBR materials" in the drop down. I'm not sure if the B2M3 material I made is the same thing. I would really like to learn how to use designer but i'm not familiar enough with all these processes to know if this is the best choice or if there is a better method using Photoshop. 

Like I said, I'm in the dark here on my own with nothing but dingy little flashlight trying to shine a light on all these complex programs and practices. I know i'll figure these things out eventually on my own, but advice definitely helps. 

Atlas tutorial I mentioned:

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