Without the description of the rest of your electrical system:
Your alternator / battery cannot provide enough current so the amplifier is creating to much heat and shutting down due to thermal
Your alternator / battery cannot provide enough current so the amplifier is going into low voltage protection mode
It appears that you have the Sound Storm SSL Evolution 1000.2 amplifier. it is an a/b amplifier. If you have your subs wired in mono, then you probably have them wired into 2 ohms, which that amplifier will not do. That amplifier will only go down into 4 ohms mono, or 2 ohms stereo.
Solution:
For testing purposes, turn the gain back to 0, then move it up to 1/3 rd
test, if it still shuts down the amplifier:
disconnect the speaker leads and wire them into only one channel, the left or the right.
test, if it still shuts down the amplifier:
get a new battery and a higher output alternator.
* please note that this amplifier is not going to put out anywhere near 1000 watts, The Gain is not a volume knob. The Gain is not a volume knob, also, please note that the Gain is not a volume knob. Never ask an amplifier to do what is it not capable or willing to do.