You are correct. Only one value for Ct and x can be specified. So if you have different systems for the two directions, going with the one which would generate a higher base shear or in other words going with the more conservative value for these parameters could be an option. As an alternative, you can directly specify the Periods in X and Z ( PX and PY ) in which case the software does not internally calculate the periods as per the Rayleigh method but uses these user defined values. The periods eventually used in the analysis are reported as part of the analysis output and that would help you to cross check as to whether it is using the desired values or not.
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