Many folders cannot easily be moved without special measures. Some advice is to simply copy the entire user profile to the other drive and then create a junction link to it so that the entire folder is moved, junk and all.
mklink /d C:\Users\UserFolder E:\UserFolder
You would copy the entire profile folder over for each user, then delete (or, for safety rename it temporarily) the folder from C:\Users before running the above command. You will have to do this as an administrator user who is not one of the users you are moving at the time, as that profile will be locked.
If you were to reinstall Windows you would first need to create all the users, log into them each individually, then recopy the profile over (so that the registry for each user is set up as new) and then recreate the links to the profile directories.
Your question regarding the folders that you can easily move such as My Documents and so on is an easy one, though.
When you reinstall Windows you will loose the link to the location that you have put the folders in, as the Windows installer will not know where the folders should be, but it is as simple as following the same procedure to move the folder as you have already done. Right click the folder, go to Properties, then on the Location tab click "Move".
You then browse to the location you have already set up and when you click okay it will tell you that the folder is not empty. At this point just click "OK" and it will copy whatever new files were in the current location to the new location. I have done this before with Windows 7 without problems.
Sadly though this does mean doing this for every folder for each user.
