Audio Systems: wireing, car fuses, amp fuse

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Question -
hello, i have a 2002 mitsubishi eclipse and i recently installed a system in it.  i had the subs wired and was working on putting my new cd player in it.  i believe i touched some wires together i shouldnt have and shorted something out.  the ecm doesnt work.  they believe it is from the remote wire from my amp the ignition wire in the back of the radio harnes.  it is a 1000 watt amp with 40 amp fuse in it.  is it possible that it could have shorted something out from the power of the amp comming threw my cd player that goes to the ecm?  they thought i should run the remote wire to the fuse block so it is safe?  is that nessacary i've never heard of anyone who does that. any suggestions or what do you think?  thanks

Answer -
wait, when you say ECM do you mean Engine Control Module?  In other words your car doesnt run now?
yes that is correct, engine control modual and my car isnt running.

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I dont think that's possible at all.  the wires inside the cd area are separate from any of the computers, etc.  they are also on fuses so they would just blow fuses if they touched the wrong stuff.  As for the amplifier wire that shouldnt have anything to do with it either.  Check all the car fuses, there should be a bank under the hood and another one inside the car somewhere,  one may be blown.  Do as much troubleshooting as you can or find a friend who's a mechanic since this would be easy for a mechanic to rip you off.
Check all the fuses and let me know.