Answer to your original question: Yes. Assuming you have chosen the correct 2 wires from the factory harness you should be holding a + and a - from the same channel (very important!). This is exactly what a single RCA plug represents: + at the tip, - at the surround.

Couple other things:

First, if you tapped into the leads before your existing factory amplifier, then there should be no need for an LOC. Confirm this by checking the voltage in the lines using a digital multimeter at various volume levels and compare to the input voltage listed in your amps owners manual.

Second, alternator whine is almost invariably the result of a bad ground. Make sure you have grounded yourself to bare metal, and ideally in the same spot as the factory amplifier that you are still using for the rest of the speakers.

To properly "tune" your amplifier you need a multimeter and you need to know the frequency at which you want to crossover. Presumably you already know the frequency, so just set that on the amp and let's move on (use an oscilloscope if you want to make sure you get it exactly right!)

Turn the gain all the way down (counterclockwise).

Calculate the proper maximum voltage for your amplifier. Voltage = square root of (wattage * impedance). Take your amp's maximum power output (watts) and multiply it times the resistance of your speaker. then take the square root of that number. This is the maximum voltage you want to see across the speaker outputs of your amp.

Now for the fun part - perform this next step with the speakers disconnected as it will result in rather loud sound levels. Connect a multimeter across the speaker outputs (in other words, touch the red lead to the + terminal and the black lead to the - terminal of your amp. With the head unit at what you would consider "max volume", slowly increase the gain on the amplifier until you get a reading equal to the voltage number you calculated in the last step.

Repeat this for each channel of the amplifier - nothing to it

d-