The dual pipes in the picture are from the duct top and not the flue, you can see the flue coming off the top with black pipe connected (it exits at the rear top of the stove). This stove is using a dual outlet duct top, which is an option, normally there is one outlet and generally uses the convection fans on the stove to push air through the ducts, you can also add inline duct fans to boost the flow for long runs.
If you look closely at the picture you can see a piece of metal blocking the normal air outlet at the front of the stove just under the top. The convection fans on the Pocono are at the rear and force air up the back and across the top, this configuration creates a plenum out of the back and top of the stove. The fans are both feeding this common plenum and do not individually feed the ducts, but rather create air flow in both ducts pretty much equally.
The hot air jacket on the other hand extends over the sides of the stove as well and omits the use of the convection fans in the back, it uses a larger inline duct fan, generally the hot air jackets use 12" or 14" round outlets to facilitate connection to the duct fan. This configuration is usually hooked to the cold air inlet of a hot air furnace, but can also be used to distribute the air to floor registers. The other attribute of the jacket is less radiant heat in the space where the stove is located, in other words more surface area of the stove is covered and putting heat into the ducts.
As you plan your system and get ideas I encourage you to continue posting on the forum and talk with your dealer as well. You can also reach us at the plant at 570-752-1811. I salute you on the questions you're asking, they'll help you stay warm this winter!