I con't be sure if this will help every time you get the error BAD CONFIGURATION FILE when trying to install a template in Prestashop 1.6. But when I got this error trying out a Leo Theme Prestashop template, it was hard to figure out why at first, in the end I found out the template file (the .zip) was somehow corrupt.
I hope this helps if you are trying to upload a template and get a BAD CONFIGURATION FILE error:
All I did was unzip the template.zip file and re-zip it.
Make sure it doesn't contain another zip file which contains the actual template.
If so then unzip that zip file, ultimately looking for the Template files themselves. Once you have the prestashop template files unzipped, I re-zipped them and use the normal method to install them. Hopefullt that will work (no more "BAD CONFIGURATION FILE" error reported)
Then the template should appear correctly available in the prestashop back office.
Hope that helps.