I am trying to make a smaller version of the MEGA-plate, but I can't understand their published protocol. I have been having troubles figuring out all the layers used (and their order) and how they fused the gels with different antibiotic concentrations at the end. I would be happy to provide more clarification to better answer this question.

Here is their materials and methods for reference

http://science.sciencemag.org/content/sci/suppl/2016/09/07/353.6304.1147.DC1/Baym.SM.pdf

And other published intructions

https://openwetware.org/wiki/How_To_Make_A_MEGA-plate

and this is the paper

http://science.sciencemag.org/content/353/6304/1147