has been answered before.
In addition to the above threads there is currently an enhancement proposal (that is not yet merged into the kwant mainline yet) to allow one to specify conservation laws in the leads. For your case of spin this will mean that the modes of the system will have well-defined spin projections and you will be able to calculate transmissions between spin up/down subblocks of the scattering matrix directly. See
https://gitlab.kwant-project.org/kwant/kwant/merge_requests/15 for details.