Generally speaking one does not install two copies of a program. Although it is possible to install both the 32-bit and 64-bit versions of calibre. They
will share the configuration.
You can also use calibre portable, distributed through calibre's website or via the portableapps.com launcher.
Re: the icons. calibre recently gained the ability to associate with files it handles via file browser ==> Open With. But only on Windows 8 which should ask what you want the default to be.