Ok, I figured this out, but I don't quite understand why it now works.
What I did in the template file was to select the cell with the "firstChart" slot. Then I clicked the Cell Behavior button and chose Evaluate and Delete. This fixed the double chart output problem, so I did the same for "secondChart" and it now worked for both. I had assumed that evaluate and delete would actually delete the output, though I didn't know why that was desirable. I now see what it does, but I still don't quite understand it.
I still don't know if I have the documentation for this report generation feature. If I click the Help button in the upper-right corner of the template notebook, I get the error:
"paclet:guide/ReportGeneration" could not be found.
But there is a guide/DocumentGeneration in the help system. I wonder if that button is linked to a non-existent guide/ReportGeneration, that was perhaps renamed at the last minute? Or, am I just missing the documentation on how to work with templates? The only thing that I can find is that video that I linked to in the first post.