Actually, if you remove the stock crossover/amp the factory wiring that was built for just the stereo is still there. I hope you didn't cut it?
The stock stereo wiring connects into the amp, then a seperate set of connectors goes to the stereo.
If you remove the amp, without snipping wires, the factory connections from under the dash directly connect to the conversion harness. The amp is just another accessory in the mix.