I installed my Koker similar to the way you describe it except I only run one blower motor at a time. When heating with coal, the Koker blower does all the work. When heating with propane only the furnace blower runs.
Here's how my system is set up:
The heat duct goes from the top of the Koker into the plenum on my propane furnace. I made it as big as possible. My air return ducts come from the main cold air return into both side of the Koker blower motor. I installed one backflow damper in my heat duct between the Koker and the plenum, one in the plenum itself and use the filters wrapped in plastic as dampers in the return ducts in both the Koker and the propane furnace.
When I heat with the propane furnace the plenum damper is open, the Koker heat damper is closed, the furnace filter is uncovered, the Koker filters are covered.
When I heat with coal the plenum damper is closed, the Koker damper is open, the furnace filter is covered, the Koker filters are uncovered.
It takes me about 2 minutes to change from one fuel to the other. And you're right, you must have the two systems that share duct work separated by dampers or you'll create a loop that will tend to circulate thru the furnaces instead of heating the house.
I bought all my material from a local distributor of "Graymetal Products" I called Graymetal for the name of their distributor in my area. They've got a very good catalog you can download from http://www.graymetal.com/products
Good luck. I hope this helps.