The generation of an expanded model is a one-way process, and there is no automatic way to merge any changes to the expanded model back into the base model. Generally, therefore, you should edit the appropriate variants in the base model, adding extra parameters where necessary.
It is, however, possible to edit the expanded model directly; the Editor will ask you to confirm the first such modification. If you proceed, the Editor will disassociate the modified model in memory from the expanded file on disk in order to reduce the likelihood of overwriting the system-generated model. Even if you force the Editor to overwrite this file, STEM will detect that the expanded model has been modified next time you run the base model and will give you the opportunity to cancel the replication in order to save the manual changes elsewhere.