Hi San,
I don’t have much information regarding theoretical aspect of the bidirectional fiber and how different it is from SMF unidirectional fiber, but in practice, both signals pass through bidirectional fiber simultaneously and in OptiSystem, the optical delay is used, so as to make this bidirectional system work.
As for what you have asked about the system design with bidirectional fiber, you can see Optisystem samples in “PON and access systems” folder, for example “CWDM PON” to see how it can be used and then use your own scheme. Then you can ask any possible further questions here.
Regards