Here is a step by step.
1.) Calculate the target output voltage. It's a pretty simple equation.
Output Voltage = the square root of RMS wattage X the Final ohm load.
Example: 1000 W RMS X 2 Ohms = 2000
And, the square root of 2000 is 44.72. In this example, 44.72 is the target output voltage.
2.) Set all of the controls for the bass, on the head unit and the amp, to zero. ( gain, boost, bass control)
3.) Disconnect the subs
4.) Turn off, or disconnect the mid and high range speakers in the car.
5.) With the engine running, pop in the 50hz test tone, on repeat, and crank the volume to about 3/4 of the head unit's capacity. If it goes to 40, turn it to 30. This is usually the point just before the signal will start to degrade.
6.) Set the Multimeter to AC voltage. Then see what you get for an output.
7.) Slowly turn up the gain, boost, and bass, until you reach your target voltage. On most amps, this is the point just before the amp starts to clip. Clipping causes distortion. Which will cause a ton of problems. Including the one that you have now.
8.) Turn down the volume and eject the test tone CD from the head unit.
9.) Turn everything off.
10.) Reconnect everything.