I was thinking there should be a PC program for analyzing variations. A large diagram in the middle of the screen for the main line with at least 2 (or more) smaller boards on the side for sub lines. No need for an engine. No need for a lot of bells and whistles. You should be able to go from the starting position or be able to set up a position, invert the board, etc.
The winboard/xboard interface is also another good program. You can not open multiple boards, but you can run multiple programs.
If you want to customize your interface, you could write a web browser interface with limited html knowledge. NOTE: M$IEv6 does not want to run any of the following scripts. apronus.com/chess/wbeditor.php provides lots of interaction. dhtmlgoodies.com/index.html? … html-chess uses HTML5, which can use the canvas and 3d viewing.