What is the proper way to hook up a stereo amp?

Without reading the name plate on your 1000 watt amp, I would guess that it will need about 100 amps at 12 volts. The amp would need to be wired straight off the battery with large enough wire plus voltage drop to carry 100 amps. That would be about a #2 wire.
My guess is that you overloaded your converter and either burnt it up or blew a fuse either in the converter or the 12 volt DC power distribution center.
Don't forget to add a couple more batteries to run the amp!