Assuming what you are saying, is that the installers bypassed the oem amp, and have the new head unit powering all your speakers, the following advice will be applicable....
The only way your new head unit is sending nothing but highs to the front and lows to the rear, would be if the head unit has such settings. Some do. Pioneer for instance calls it FIE. This creates decent imaging by splitting the frequencies up in a manor that is conducive to a good sound stage. With your speaker set up though, this is not ideal.
I have yet to mess much with the stock amp, but would imagine the following is true. The oem amp has several channels of amplification (like ten). Each one of those channels is crossed over at a specific frequency for each speaker. Your head unit's amp has four channels of amplification. Without the use of seperately purchased aftermarket crossovers, there is no way I am aware of to run all speakers off your new deck.
I would normally recomend sticking with the oem amp, until you replace all the speakers. The reason for this, is the new speakers for the front for example will come with it's own seperate crossover (if of course you buy two-way or three-way seperates for the front).
The rears you bought are fine, you just need to either turn off the internal crossover on the head unit, or make sure their is nothin in between the rear speaker lead on the head unit and the rear speaker. :wink
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