Well Willis, the stereo shop is also in the business of selling amps, the price might be the same but the profit margin might not be. 
But a new bose system in a stock car is certainly nothing to be proud of! They are notoriously terrible. I have a bose system in my $100k car and I guarantee my stereo in my LX450 sounds better, has better bass response, can be much louder and the mids and highs are clear.
Lots of ways to skin a cat, but like I said if you're going to run two amps in the back, you will need to run a lot more heavy gauge power wire, speaker wires, RCA cables, distribution block, etc. If you are really going to run two huge amps, are you upgrading your alternator? If not you will probably get dimming issues as well as amps that can't support their full power.
The biggest 12" sub I saw on Alpine's site is 1000w-3000w so lets say the installer is going to power it with 1200w, that is 83amps at 14.4v, I believe the 80 series alternator is only rated at 80amps....
There are some great audio shops out there, there are also some that don't do much research and just try and sell you the most expensive components without looking at the system as a whole. He might not know that the 80 series alternator is pretty underpowered compared to most new SUV's

But a new bose system in a stock car is certainly nothing to be proud of! They are notoriously terrible. I have a bose system in my $100k car and I guarantee my stereo in my LX450 sounds better, has better bass response, can be much louder and the mids and highs are clear.
Lots of ways to skin a cat, but like I said if you're going to run two amps in the back, you will need to run a lot more heavy gauge power wire, speaker wires, RCA cables, distribution block, etc. If you are really going to run two huge amps, are you upgrading your alternator? If not you will probably get dimming issues as well as amps that can't support their full power.
The biggest 12" sub I saw on Alpine's site is 1000w-3000w so lets say the installer is going to power it with 1200w, that is 83amps at 14.4v, I believe the 80 series alternator is only rated at 80amps....
There are some great audio shops out there, there are also some that don't do much research and just try and sell you the most expensive components without looking at the system as a whole. He might not know that the 80 series alternator is pretty underpowered compared to most new SUV's