You will have to update AE CS6 to version 11.0.4 to work on anything past Mountain Lion.
Motion Sketch will not work.
RAM preview will not play correctly on first playback, but once it loops it will play smoothly.
Those are the only two issues I know about.
That being said, what do you hope to get out of El Capitan? It might not be worth the hassle of jumping up that far. People are complaining about Mac's latest OS's. Yosemite and El Capitan both have had some pretty bad blowback. Maybe just go up to Mountain Lion or Mavericks?
And, of course, make a Time Machine backup now in case something goes awry in your upgrade process or you don't like it and want to go back.
Thanks very much. I need to upgrade to Safari 7 to work on Wix. Maverick I believe works like you said. One last question do you know where can I download maverick? I can't find it at apple.
If you don't have any machine that was ever put on Mavericks, I don't know if you can get it anymore. You can try a Google search though. Some people may have some ideas.
Anyway, other than the two things I mentioned, CS6 should work on El Capitan if you have to go that far. See Adobe's official note on the subject: After Effects and Character Animator ready for Mac OS X v10.11 (El Capitan) | After Effects region of interest