Best way to store custom commerce pane form data as part of an order?
I have had the same issue for some time with field collections and simply switching the panes on and off in the order entity was not doing the trick.  I ended up being able to work up a solution using order types.  http://drupal.org/project/commerce_order_types

In addition I want to mention that we used the following patch: http://drupal.org/node/1887812 so that commerce could recognize panes from different order types.  At this point your already there, its a simple process of switching order types and subsequent panes based on the order type.