I run calibre on both a W7pro desktop and a W8.1 laptop, sharing the library using Dropbox. Both the library and the configuration directory are in dropbox. The dropbox folder the same path on both machines. I start calibre using a .bat file that sets the CALIBRE_CONFIG_DIRECTORY environment variable then starts calibre. This all works well, keeping in mind the usual caveats about dropbox-shared libraries.
I do not use a microsoft account on my laptop. I tried it and I didn't like it (don't remember why). I never use the "store" so don't miss it.
The path to my account (c:\users\charles) is the same on both machines. I can't say whether "Documents" will be the same because I sync mine between computers using my local Synology NAS.
FWIW: I use the Win8 tool "Classic Shell". It might not be necessary with Win8.1, but it was a lifesaver with Win8 and I am used to it. I never use the Metro interface. Well, almost never. I do sometimes run the Freda ebook reader in it with my laptop converted to a tablet.
EDIT: for Kindle for PC, I downloaded the installer from
http://www.amazon.com/gp/kindle/pc/download and ran it in desktop mode. It created the normal folders in documents. I downloaded a book from my amazon library and it appears where it was supposed to. I added it to my library and the Alf plugins did their thing without problem.