Hello Budo,
Yes, SMH is the good way to add sources of water, like rain (you can see how rain is treated). SMH is taken into account in the tracer equation, so this should not alter the tracer treatment (see also logical value YASMH). You can also look at punctual sources, which are given through their coordinates, discharge, values of tracers, etc. You can see in DIFSOU how they are taken into account before a call to CVDFTR for advection-difusion. You will see also that depending on the fact that you bring or take water, the corresponding value of tracers change.
I hope this helps,
With best regards,
Jean-Michel