Hello Arup,
You would open Profile Designer and add the material. To ensure it is added to Master you need to add it to the correct section of the tree browser on the left side of the window. When you first open Profile Designer you will see your current design file expanded in the tree. You need to expand the section called Master (see attached picture). Once expanded you would add the material here the same as you would add any material.
Could you clarify what material you are trying to add? Epsilon-1 and Epsilon-2 are not a notation I am familiar with, are you attempting to add a complex refractive index or a nonlinear material?
Scott