Some factory amplifiers are designed to work with a stereo that outputs a signal higher than line level, i.e., slightly boosted.

If you check with your local install shop, you might be able to find a factory-integration device that boosts the signal to the factory amp. For instance, on my friend's Dodge Durango, he used a PAC OEM-1 interface purchased from www.tune-town.com to do this job. Don't know if they have one for your particular make and model of car, so check.