Well either before or after will be high level signals. But the signal is amplified obviously after it has went through the amp.
The deck controls the input to the monsoon amp, which in turn controls the output of the amp so I'm not sure what you meant here.
Really my concern is does the amp change the signal that is being sent out? Like is there a crossover point after the amp that is designed for the 6X9's? Obviously they couldn't handle very low frequencies like a sub could. I've spliced after the amp as of now but the amp I won off ebay was shot so I'm getting another amp right now so there's no way to test this. I was just thinking that the signal may be altered by the monsoon amp to protect the small stock woofers.