Problems finding voltage between two points (transistor)
I tend to think of these types of transistors as a faucet.  Water (current) goes from the tap (base) to the drain (emitter).  Your faucet has a valve on it that changes the flow of water (current).  You use that resistor in the circuit to control how much current goes into the emitter, just like you would use a valve to control the tap.
If you think of it that way, then when Q1 is biased properly, the valve is open and water (current) is flowing relatively freely to ground.  BJT's are current controlled devices.  Since there is not much difference between ground and the base, then I would put my negative lead there.  The positive lead would go on the collector.