Does it matter?
If all voltages "seen" by the sensor and BBB are within spec, then you're not doing something "wrong."
If one of the chips will "see" a voltage above VDD or a voltage below VDD, then you'll probably let the magic smoke out.
To figure out which voltages are "seen" by the chips, just do the resistive divider math, checking all the hook-ups.
Remember to account for the source impedance of any output pins involved!
So, for example, if your sensor is connected to +5V and GND, and your BBB is +3V and GND, and you have a -5V rail, and you connect a 2:3 voltage divider to the output of the sensor:
When the sensor is at full output, the voltage across the divider is (+5 - -5) or 10V. The voltage at the division point relative to -5V is (3*10/(2+3)) or 6V. The potential relative ground is 1V.
When the sensor is at ground output, the voltage across the divider is (0 - -5) or 5V. The voltage at the division point relative to -5V is 3V. The voltage potential relative ground is -2V. If this is hooked into a BBB input, it will fry that input.
So, if I understand your question correctly, you probably want to divide between the output and GND if you're forwarding the signal to a single-ended GND-referenced analog input pin.