The code presented in the Embed Code window is generated internally by JuiceboxBuilder-Pro and has nothing to do with the 'template/index.html' file. The 'template/index.html' file is used only to generate the output 'index.html' file (in the gallery folder). There is nothing you can do to change the code which appears in the Embed Code window.
You can modify the 'template/index.html' file, though, and any changes you make to this file will be reflected in the gallery's own 'index.html' file once you save the gallery.
On Mac, it looks like the 'template/index.html' can be found here: /Applications/JuiceboxBuilder-Pro.app/Contents/Resources/template/index.html (although I do not have a Mac to check this path)
On PC, it can be found here: C:\Program Files (x86)\JuiceboxBuilder-Pro\template\index.html
I hope this helps to clarify things.