Although this may not have been true in the past, file management is really something that should be left to the application. Strictly speaking...there is no real use case where you should have to move or manipulate any D-Tools file using Windows Explorer. My responses are in line with your questions\suggestions below...
1. This should work. If the files that you are adding to the projects are not getting checked in to the server and made available to the other users then I would say that something is wrong in your configuration. I suggest that you contact support and have them take a look at it for you.
2. To remove a file that you have added to a project you just need to check the project out and then right click on the file you would like to remove and select "Delete". Then check the project back in for the change to be registered with the server.
3. What is your true intention here? Is it to be sure that you have a backup of the files in case something happens to your machine or is it so that you can restore a project\drawing to a specific point?
If your intention is to simply be able to restore a project to a specific point in time then thats what revisions are for. Renaming the project or doing a save as is going to do nothing but give you grief. With Revisions you can restore the project and all associated files to a specific point in time. You can also rename them and give a brief description.
If your intention is to backup the file in case your machine dies then saving multiple files isn't really achieving what you want. Your best bet in this case is just to be sure that you hit "Save" as often as possible and "check in" the project when you are done with it. Then if something happens to your machine you only stand to lose the work you have done since the last "check in". To be double sure you can also use the built in utility to backup your server and that will cover you in the case of a server failiure.
4. This is a known issue that will be resolved in a future service pack. See this link for more information on how to work around this problem:
http://www.support.d-toolsblog.com/s...drawing-files/
Hope this helps...good luck.