scotty v

I stripped down my previous ride and transplanted only the subs and amp into the cl. I am running a kenwood excelon amp and 2 12" Boston Competitors (2 yrs old). I read many posts on here about running subs off of rear 6x9's an followed suit. I bought the small adapter to aid in sending the signal to the subs from the 6x9's. I then ran everything else how you are supposed to (Actually 23 did everything!!). Then the other day, the subs just stopped working -but the stereo still works. The amp light was flashing for protection mode. I talked to some "stereo genius" that said that it is bad for the amp with a signal from 6x9's instead of RCA's from the headunit. He also said that it could have fried from the ground being longer than 18 inches (mines about 3 feet). I'm not sure if the amp is done, but we are going to open it up soon and take a look.
sorry this is so long, but i'm pissed - any suggestions or informational comments on this problem.
Thanks