If you install a wood stove below the neutral pressure plane of the house (usually the case with a basement install) then you usually create a chimney flue that will backdraft and keep your house nice and smokey and filled with potentially deadly fumes. If this is combined with a cold, outside chimney or chase then it is even worse. If the chimney doesn't stick up above the peak of the house then it is even worse and you will probably never get it to draw. You need to engineer the whole thing correctly to avoid a smokey backdraft situation. see: http://www.nrcan.gc.ca/es/erb/reed/wood/07_e.html http://www.woodheat.org/evilchim.htm
To answer your questions: 1. I don't think metal vs. flexible will make any significant difference since they are both insulated. 2. Heating the crawl isn't your answer. Your furnace is only putting out so much heat, dumping a bunch of it into the crawl is only going to lessen the amount you have for living spaces and your furnace might also not be up to the task. 3. Are there return air ducts inside these two bedrooms? If not, either put one in each room, equaling the total size of that room's supply ducts, or, cut 1.5" - 2" off the bottom of the doors to these rooms to facilitate air circulating back to the central return, or, put in flow-through grilles in the partition walls to accomplish the same thing. If this is not the problem then you could put more insulation under the floor. I would consider 2" rigid "celotex" polyisocyanurate foam sheets. If there is a bigger problem then you may just need to bite the bullet and retrofit zones into your house using trolatemp system or similar. Sometimes you can get away without this as it is expensive, by using your dampers to balance your system better. Do not attempt to balance the system using the register dampers in the rooms b/c its too late by then and you just create backpressure. I would add insulation and adjust main supply dampers to correct your situation.