SMOTE on training data
Even I'm also not sure about Weka, but so far I read, it provides functionality for data mining, data pre-processing, model training.

Generally what I do,

In case of pre-processing: model generated after pre-processing of training data(it includes SMOTE data), I save this model. Saved model is used to pre-process test data.

Let me know in case, you are expecting something different in answer.