Now I get the picture. You want the original windows, or a specific windows, to always be visible. One method is to have dual displays, but I think you would have tried that it you had two monitors.
Off the top of my head I don't know how you tell windows to keep on DOS box on top. But you can tell the CMD to start a program with a limited windows, or no window. Look at this:
START
Start a specified program or command in a separate window.
Syntax
START "title" [/Dpath] [options] "command" [parameters]
Key:
title : Text for the CMD window title bar (required)
path : Starting directory
command : The command, batch file or executable program to run
parameters : The parameters passed to the command
Options:
/MIN : Minimized
/MAX : Maximized
/WAIT : Start application and wait for it to terminate
/LOW : Use IDLE priority class
/NORMAL : Use NORMAL priority class
/HIGH : Use HIGH priority class
/REALTIME : Use REALTIME priority class
/B : Start application without creating a new window. In this case
^C will be ignored - leaving ^Break as the only way to
interrupt the application
/I : Ignore any changes to the current environment.
Options for 16-bit WINDOWS programs only
/SEPARATE Start in separate memory space (more robust)
/SHARED Start in shared memory space (default)
http://ss64.com/nt/start.html
Example"
start "Peek-A-Boo" /MIN "new-batch.bat "
Would tell CMD stat new-batch with a window in the task bar that says "Peek-A-Boo" but not on the screen.
That is the best I can do. For more info, see the link above.