I just bought this furnace.. And I want to install it as a downflow.. Do I just flip the whole furnace upside down? Looks funny that way!! Just want to know before my installer screws this up..

No. A furnace MUST be installed the way it was made, if it's a upflow/horizontal means it can be installed upflow (supply out the top) or horizontal left. Downflow is downflow, upflow is upflow. An upflow will not work flipped upside down, because of the exhaust venting. And again, a Upflow furnace is DESIGNED for upflow and most commonly Upflow/Horizontal install.

Since switching over from air to heat, the furnace operates as it should. The next time it should cycle it will not, if you turn the thermostat off and turn it on again, it will cycle. I have tried a new thermostat and it does the same, all filters are new and furnace was put in last fall about this time and worked fine.

What does this have to do with the posted question? If this is a separate question, post your own and don't piggyback since few people will see it.