Also, in response to your original question, if you decide to continue working with CMAQv5.2, then yes, you should use this setting in your run script if your MCIP files define a 29 layer vertical structure but your emissions were processed such that all mass was allocated to the first six layers only and the resulting gridded 3D emissions file only has 6 layers, corresponding to the lowest six MCIP layers.
This earlier thread contains some additional context on the use of the CTM_EMLAYS variable in earlier versions of CMAQ. It also notes that CMAQ’s emissions interface was changed substantially in versions starting with CMAQv5.3.