I just bought a honeywell rth7000 thermostat, to replace my old manual thermostat.
My old thermostat only has two wires, black and white.

On the old thermostat the was wire was connected to "E" and the white had no label. Both wires were connected to RH at the furnace in different location..
Not sure where to connect black and white wire on digital thermometer...

I don't really understand your statement but I will tell you that he two wires should connect to the RH and the W on the new thermostat. It does nt mater which wire goes to which pole on the thermostat. Still I don't undertand the "Both wires were connected to the RH at the furnace" but if you did not move them the thermostat should work.