Best install practices?

[BBFG#]

I just upgraded from 5 to 6 and decided to start fresh by uninstalling and clearing out so many files in multiple folder locations. The Options button still only has a single path to set to and it defaults to Program Files (x86). Which I simply removed the (x86) to put it in where I believed all the 64 bit plugins go. But after install, I noticed it still puts a copy of the same files in the (x86) folder anyway. The only difference being that one has two additional folders. Can I safely delete one of these locations? And which is the one that's a must?
It is a much cleaner install than it's ever been though.