That sounds very… complicated.
I’ve come across 3 different techniques for using texture atlases. If you are looking for packing tools to create them, I know they exist, but don’t have enough experience to offer any advice.
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Lay out the object UVs in your DCC package relative to your texture atlas (create your UV map specifically to make use of your atlas in the way that you want). Very manual, but very efficient.
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Use the textureCropping function to isolate the different parts of your atlas in a material
https://docs.unrealengine.com/latest/INT/Engine/Rendering/Materials/Functions/Reference/Texturing/index.html#texturecropping
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Use the ‘Merge actors’ tool to combine meshes together, and create a combined texture atlas from their respective textures
Does that help, or have I misunderstood your question?