Don't overthink and overcomplicate matters. None has to do with the other. Separate versions always install to separate folders. It has been so since forever. Upgrades will ask for a secondary serial number as verification when installed without a previous version present. Your FB issues are a completely different matter and may relate to having had the FB Beta on your system. Check the FB forum for specific instructions.
I deinstalled CS5.5, run a windows cleaner program and restarted Windows 7.
And started the CS6 installer again. Now only FB 4.6 and Acrobat Reader Prof
were checked automatically to install. I done it.
Now I have what I wanted. Only CS6 Programs including
the new Flash Builder Version 4.6