Hi Wesmitchell,
Yes, you should be able to run these applications together. As you are getting error 'Error code 49' while trying to update Illustrator CS6 and have tried some steps to resolve it.
I would recommend uninstalling the app and reinstalling it again, you may use the following link to download and install it: Download Adobe Creative Suite 6 applications.
After this directly download the update patch for Illustrator CS6 from here and install it: Adobe - Illustrator : For Macintosh , Adobe - Illustrator : For Windows.
Let us know if this helps.