Ok, the topic is lying a bit. But its a work around that works like multiple layers should do.

Step 1
Take your favorite encoding and open it in a editor. Now select all glyphs, copy it and paste it to the end of the same encoding file. Now add to every glyph a period.

sample

A
B
C
A.
B.
C.

In fact you have doubled every glyph of your encoding. These gylphs will work as your "layer".

Step 2
Now you have to open the Groups.txt and use the same trick to assign these new gylphs to your standard glyphs. I have done it with Excel and saved the text as tabulator divided text.

sample

A A.
B B.
C C.

...

Now you can switch by double clicking on the shape group to get to your new "layer". (Please enable "Double-click to edit neighbor or sahpe gylph group" in the FLS prefs.) If you need more layers, you have to do the same steps again. A three layers encoding would look like this:
A
B
C
A.
B.
C.
A..
B..
C..

The Shape groups file would look like this:

A A. A..
B B. B..
C C. C..

Instead of .. you can use other gylphs like : ; but dont use , (comma)!

So, in the metrics window you can work with the first layer like before. If you need to set some samples to compare your different designs/layers, it should look like this.

Hamburgvons \n/H./a./m./b./u./r./g./v./o./n./s.

BTW. The extension pattern to use a period is a first hack. Adam & Yuri will hopefully find a setup that is compatible with all aspects of FontLab & Phyton. The simplicity of this solution is plausible, the file format of FontLab needs no special treatment to store layers and the format stays compatible to earlier versions.