Ooooh, this sounds super fun!! Doing it manually is certainly going about it the hard way but it's actually the most rewarding. Just my kind of thing.
Taping the two markers together will not create a stereoscopic effect. The reason it wont work is because it's not about the markers but having two flat images that are viewed at different angles. This is because of the illusion of perspective from having binocular vision. It's also important to get the colors right or the glasses wont work. It's a subtractive color so it has to match the glasses.
This would be very difficult to do manually without using some kind of reference. For this you could use some software to generate the images and then use those as reference. I use Blender which is free and open source and it can simulate reality. With this software you could use two cameras offset for binocular disparity and then import your drawing and take a picture from each camera. Of course, you can do this with two cameras in the real world as well.
Another way that might work but isn't as much fun is to use an anaglyph background. My sister always finds the best gifts and she gave me this anaglyph sketch pad. It's really cool, just draw with regular dark pencil or black ink and your drawing is floating above a 3D background! Perhaps you could replicate this on your whiteboard?
https://3dvision-blog.com/3006-3d-drawing-pad-is-a-very-simple-but-ingenious-product/
Please, let me know what you come up with?!
