Did you put the OEM replacement on if so check the wiring make sure the purple wire is on the common side (marked with a "C" usually has a red wire on it too) of the capacitor and the brown is on the fan side. If these are backwards the motor will run backwards. If its a universal replacement...
The thermostat will work fine you need to hook the Red wire to the Rh terminal and the white wire to the W terminal also make sure the dip switshes or jumpers are set for gas heat and it should work fine. the thermostat will have a 5 min delay when you turn it on if you see the heat logo...
best way is to set a package unit on the ground behind the garage and cut return in thru the block. Then run the supply up the wall to the ceiling height. Punch thru wall and run a simple trunk line across the ceiling. Another option is to run a split system in the attic if you have room.