im not sure why everyone is dogging on the bast boost. for me it doesnt seem to make sense to recommend getting a bigger amp (double the wattage) and then say to not use the bass boost. all youre doing is upping the total wattage on a narrow band of frequencies instead of the whole range...so why would that be "worse"? most modern amps will not clip or distort with the bass boost up and the gain at 40%, period. just do what sounds good to you.
as for the problems, im thinking you have two seperate (but related) issues.
the amp is shutting off. this can happen for a few reasons: a short or low resistance (cause by incorrectly wiring the subs to too low of a total impedence or touching speaker wires), overheating, or voltage issues. as others have mentioned, double check your wiring to make sure everything is secure and not shorting/grounding out. also, make sure the amp has plenty of ventilation. does it feel very hot when it shuts down? last, check the voltage at the amp with a DMM (if you dont know how..ask...its very easy). the voltage should be between 12.5 and 14.5 depending on if the car is running or not. anything out of that range points to a deeper electrical problem. test the voltage at the battery and you should get a reading in the same range (probably slightly higher than at the amp). make sure the battery terminals are tight and clean. i had a problem in my eclipse where i thought the battery kept dieing, but it turned out my negative battery terminal was slightly loose and the car wouldnt start 30% of the time. naturally, its possible that the battery itself has bit the dust, leading to all kinds of funky electrical crap (including making your amp shut down). get it checked for free at autozone. if everything checks out, the amp could be at fault. remove it from the system (or disconnect the ground and RCAs to eliminate it from the electrical) and see what happens.
also...i hope you are running the remote wire from a switched source and not from a constant 12v+. that would explain your issues as well, lol. good luck!