I have trouble with preview mode in Indesign CS6 after the upgrade to OS X 10.11. The document does´t show on full screen, and the top of my desktop picture is shown at the bottom. I have trashed the preference file, but it made no difference. The dock and menubars are not on hidden automatically.
As mentioned in countless other threads, CS6 is not supported under El Capitan. Even CC users are having problems.
Sorry, but you're pretty much on your own.