LayerOptics is meant to calculate optical coefficients starting from dielectric tensors computed for bulk materials regardless of their atomic morphology. This tool is particularly useful in case of anisotropic systems in which the off-diagonal elements of the tensor are non-negligible. Is this the case of your material? Is it a monoclinic or triclinic lattice?
To answer your specific questions, you have to bare in mind that LayerOptics always assumes the presence of a substrate, whose dielectric function is hard-coded (in the current distribution we inserted bulk silicon, but this value can be changed by the user), and a vacuum layer on top. So if you are going to input only one computed dielectric tensor, you will need to insert "1" when you are asked to provide the number of layers. Concerning the thickness, the idea is to simulate interfaces at the nanoscale. This could be the case of a molecular crystals, which are usually grown in samples with a certain thickness. In general this value does not impact much the final result, except for absolute value of the optical coefficients. We recommend the user to choose values around 10 nm.
I hope these indications will help you solving your problem.