Voltages, being a potential difference are always measured relative to another voltage. Normally that reference voltage is referred to as ground, though may not always be.
The + and - on the battery refers to the polarity of the battery not the polarity of the voltage.
For instance, relative to the - terminal the positive terminal is 12 volts higher, or +12V. Relative to the + terminal the negative terminal is 12V lower, so -12V.
When one of your battery terminals is connected to a point in your circuit nominated as ground (the - terminal of your battery in this case) then your battery voltage at the + terminal is measured relative to ground, which we say is 0V. So the + terminal is 12V higher than the - terminal, and the - terminal is 0V, so therefore the + terminal must be 12V with respect to ground. The - terminal, since it is connected to ground is at the same voltage as ground, so it is 0V with respect to ground.
If you were to connect the + terminal of a battery to ground instead, then the - terminal would be 12V lower than ground, so would be -12V with respect to ground. The + terminal would be 0V with respect to ground.
-12vin a battery, it isGND. So all-5vand-12vyou have there areGND. Unless it is an ACTUAL negative voltage derived from the same power source, then it is irrelevant