I have just bought a new programmable themostat and in the directions it says it is not compatible with a mulistage furnace.
My furnace is a Lennox Pulse.

I have just bought a new programmable themostat and in the directions it says it is not compatiable with a mulistage furnace.
My furnace is a Lennox Pulse.
If you still have the receipt, you could take it back and look for the correct model for your furnace. Check the manufacturers website for possible technical advice and maybe a toll-free phone number. That worked for me with Hunter.

You may be able to select a program in the furnace by setting switches on the circuit board to control the stages. That is how my 2 stage Bryant is set up with a single stage thermostat. You would need to consult the installation manual for the furnace.