DC3 Dave
As I understand the arrangement it will still be a franchise operation whereby Stobart Air choose which routes to operate themselves at their risk and these are marketed through Flybe under the Flybe brand in the same way that, for example, Loganair operate routes of their choosing under their franchise agreement with Flybe.
It could be the case that coincidentally (and possibly mutually beneficially) Stobart will wet lease on an ACMI basis Flybe E195s to operate some of their routes, although I have no firm evidence that this will be so and cannot quite see that Flybe have the availability to provide these. The commercial lease arrangement would presumably be similar to that which Stobart Air could make with, say, Jota Aviation to operate their flights on an ACMI basis and would be outside the actual franchise agreement between Stobart Air and Flybe.
An alternative would be for Stobart Air to obtain appropriate aircraft, perhaps through Propius, for the new routes and add these to their AOC to be operated by their own crews but still marketed by Flybe under their brand.