The idea of "high level" of your aftermarket amp, and "high level" of the inputs on the Infinity amp are (as you discovered) two different things.

The infinity amp in your Jeep accepts inputs that are somewhere in between line level and speaker level. They are essentially line level that's been boosted a bit. The factory head unit's outputs are boosted to the exact amount that the Infinity amp expects. This is a totally different level than aftermarket stereos are designed to output. They do this on purpose, just to screw us up when we try to install aftermarket components.

The aftermarket amplifier is meant to take full-blown speaker inputs, with your already-fully-amplified head unit trying to supply enough power to move real speaker cones. Either that, or it's meant to take line-level input that's not amplified at all. But it doesn't have inputs designed to take the in-between outputs from your factory Infinity head unit.

The solutions to work around this are:

a) Dump the Infinity amp and the factory stereo altogether. Use the aftermarket amp the way it was intended: With an aftermarket head unit. Either with a fully powered head unit going into the speaker inputs, or with a line-level output from the head unit going to the amp's line-level inputs.

b) Connect your empeg (or any aftermarket stereo for that matter) to the infinity amp using an in-between factory-amp interface such as the PAC OEM-1. This is covered in the Installation Notes section of the empeg FAQ.

I've never heard of someone who wanted to keep the factory stereo and just upgrade the Infinity amp, so I don't know how you would do that (if that's what you're asking to do).