I've mapped Ctrl to the big middle-lower thumb key on both sides; and Alt to the smaller middle-upper thumb key also on both sides. Space is right thumb rightmost big key, backspace is left thumb leftmost big key. Windows key and Delete are small keys; and do require a bit of a reach of the thumb. But I don't use them much (e.g. for delete, I'll do Ctrl+D). Enter I put in its usual place (i.e. not a thumb key). In Emacs I use Ctrl and Alt more than Enter, Space and Backspace. And I like to press them with opposite hands like shift, hence I have them on both sides. This helps avoid stretching.

When exported as a text file from the Advantage2, my mappings look like this:

  [=]>[`]
  [tab]>[\]
  [caps]>[tab]
  [up]>[down]
  [down]>[up]
  [`]>[=]
  [lalt]>[lwin]
  [ralt]>[delete]
  [\]>[']
  [lctrl]>[lalt]
  [delete]>[lctrl]
  [rctrl]>[lalt]
  [enter]>[rctrl]
  [']>[enter]