John,
The main (intended) use for the double shoe was, as Fuwen describes, to accommodate the viewfinder and bubble spirit level when using the 12mm and 15mm VC lenses.
However, there's no reason why you couldn't use both for viewfinders. It's a toss-up which one should go in the centre. Theoretically as the shift in perspective is going to be greater at closer quarters, you'd put the 28mm finder as close to centre as you can - the 90mm finder offset would have minimal effect - but on the other hand, the perspective on the 28mm is such that a little offset would hardly be noticed. best put the camera on a tripod, check out what you see in the viewfinders in the alternate positions, note it down, take a couple of reference frames and see if there's any detectable shift between what you framed and what you recorded.
I'm actually using one for portraits at the moment on a Perkeo II 120 folder to hold a Kontur viewfinder and a Voigtlander rangefinder. The rangefinder is too wide to fit alongside the Kontur so it's attached to one of those short flash swivel fittings which raises it just enough to clear.