You can try turning off autohide menu bars in the general system preferences but…
CS6 is not supported under El Capitan.
Sorry, but if this was so critical why would you “upgrade” an operating system without checking on this first.
It's possible that memory has nothing to do with the problem. I've seen that message when working on a file on a server and somebody renames a folder, moves a folder, or otherwise affects the path to the InDesign file. Often the only fix is to force quit and re-open, but sometimes doing a Save As... to a local folder instead of a server folder does the trick.
I have the very same problem. (ID CS6 on El capitan). Yesterday I trash Indesign preferences and then disable "Application Frame" under Indesign Window menu. So far so good, no more out of memory massages, missing undos and blank screens in Indesign all day. Todays workflow was pretty same as yesterday, so I hope this is solution.
I was having the same problem… came across this article that helped. Able to export PDFs without any problems.