After upgrading to Yosemite on the Mac, I couldn't get Indesign CS6 to operate. When I opened it I didn't get a splash screen, or panels. Drop down menus were initially active, but as soon as I clicked on one, everything became grayed out. I had to force quit from the Finder. Oddly, Photoshop, Illustrator, Bridge, Acrobat, Lightroom work just fine.
I de-installed and re-installed Indesign three times, each time trashing preferences but nothing worked. I upgraded Java, but that had no effect either.
Quite by accident I found a solution. Look at (or place) the Indesign icon in the Dock. Right click on the icon and choose Options > [Assign To] This Desktop. Presto! Everything works perfectly (so far ). I hope this is useful as I understand other people are having problems Indesign and Yosemite (maybe El Capitan too?).
Mac Pro mid-2010