How to use multiple modes in HFSS?

Dear all,
I need to calculate the reflective effectiveness of multiple-layer structure. The Floquet ports are set and then the S parameters are calculated. The S11 can be acted as the reflective effectiveness. If there is only one mode excited in Floquet ports, the S parameters are 2*2 matrix, however, if multiple modes (for example, N modes) are excited, the result S parameters are (2N)*(2N) matrix. How to understand this S parameter matrix? I need to transform the S parameter matrix to transmission matrix T. How to do for the S parameter matrix result from multiple modes?

Thanks