When you are applying that metadata template to some images, it evaluates each variable at the time you are applying the template so if those source fields are empty, that is what gets written into the metadata for that image. Some options for you that I might suggest:
Option A) Don't apply this metadata template until all the other source fields that you are going to be entering data into are filled in (Possibly the most efficient option)
Option B) If you uncheck the checkbox next to a field, it will not evaluate the variables in that field. You can then re-apply the template at a later time, checking the box if you know the data from the source field has been filled in (and possibly unchecking the box for other fields you don't want to be overwritten)
Option C) Create a few different template "snapshots" (presets) for each step of your workflow, i.e one to apply copyright, and a different one to apply location data once that has been added.
Does that make sense?
Mick