no differance between upflow or downflow,Well on the upflow the a/c coil is on top the furnace and with a downflow the evap coil is on the floor with furnace sitting on top of that. I would stick with the crawl space duct work as long as it is all steel duct,sealed,insulated, and no airflow problems in rooms.BUT I dont know what the conditions are with the crawl space duct.

well for heating it is always better to heat from the floor up. My self i would go with the down-flow. the return air bends would not be to bad if they do it right
If the return duct if flex, they might want to over size it to make up the difference of the turns. If it is metal ducts they could always use turn vanes in the duct. Keep in mind that the wall between the house and garage might be a fire rated wall. If it is you would have to use fire dampers. The burner intake air
has to be at least 18" in the air. Later paulbm

Down flow is great for heating. However, Placing the duct in the attic is better for the A/C.

U can also place every thing in the attic clearing up space in the garage.

This web site has simple installation details that might help.

Here is a link that might be useful: Installation details.