CS6 is unsupported under El Capitan.
Of turning off auto hide menu bars doesn’t help then you’ll need to roll back to an earlier operating system or move to Creative Cloud.
Unfortunately, InDesign CS6 is incompatibile with El Capitan. Many people have reported this problem. The software is four years old, is end-of-life, and will never be updated. You're basically on your own.
Your best bet is rolling back to a previous version of Mac OS X or upgrading to the Creative Cloud.
Move InDesign preferences on your desktop and retry…