Try these steps:
Disable autohide menubars.
Hope for the best
CS6 has reached end of life and is unsupported under 10.11.
That sounds nice but I can't open it to get into the preferences. Also I've read recommendations that you should go into the library files to trash some of the preference files. I've tried this but there aren't any.
Also does the final comment indicate that the program doesn't work under 10.11?
CS6 is not supported under 10.11 and there are LOTS of reports of program incompatibility.
To trash the prefs, see Replace Your Preferences and Access hidden user library files | Mac OS 10.7 and later
It indicates that you are on your own. I'm sorry, but if you can't get things working acceptably, you'll either need to roll back to Yosemite or upgrade to Creative Cloud.