The ".EXE" files of the applications have their own flags to indicate whether they're 32- or 64-bit, so the system will recognize them properly no matter what folder they're in. You can put everything into one folder on your E: drive if you want.
I think the reason Windows creates two "Program Files" directories is in case people want to install both 32- and 64-bit versions of the same program. For example, when you install 64-bit Photoshop into the "Program Files" folder, it also installs the 32-bit version into the "Program Files (x86)" folder.
Unless you plan to install multiple versions of the same program on your E:, one folder should work just fine.