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I'm trying to upgrade to a 10 square and a 1000 Watt amp how do I go about hooking it up to the factory hu and keep everything still working

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Here are a couple of threads you can read over for some info on what you want to do, but there are LOTS of ways to skin this cat...

What is the stock head unit capable of?/ - Powerstroke Nation
Just looking for a little clarification - Powerstroke Nation
? on hooking up amp to stock head unit - Powerstroke Nation

I wish I knew more about the newer systems, but I am assuming that they are still not aftermarket friendly, specially since they seem to always be cutting the aftermarkets throats by adding more and more "fancy" features stock.

So assuming the Stock HU doesn't have any RCA outputs for hooking up an amp you will have hundreds of choices on where to go, mostly based off budget.

1st stage:

High level inputs on the amplifier itself. This will require nothing but some speaker wire and the supplied harnesses that should come with the amplifier if it does indeed have High level inputs (sometimes refered to as speaker level) This will just require you to split into one or 2 of the factory speaker wires and feed the amp with this signal. This will link you subs to whatever channels you splice into, so say you splice into the rear channels, if you fade it to the front you will lower the sub output.

2nd stage

This would be purchasing a Line out Converter, which could range from $5 up to a couple hundred. The basic version of this will be the same as stage 1 except for amps that don't already have the converter in them. the higher end units might come with some EQ capabilities and will be powered to boost the signal fed to the amp (make it cleaner)

3rd Stage

This would be external sound processors. These will most likely completely remove the factory HU tuning functions (not that they are much, fade/balance and treble/bass) These range from a couple hundred to over $1,000 and can turn your stock HU into a competition ready stereo (mines some actual CD reading benefits you can get from high end aftermarket units) Sometimes these will have tradeoffs where you can't use your factory volume control, and might loose some channels, but others will give you great benefits. Will require a bit of research on selecting the best unit if you wish to go this route, and will be more involved in installation and tuning of the unit when its all said and done.

For me personally I think if I were just wanting to add in a single sub and an amp to run that sub and Nothing more, I would go with the stage 1 setup, and use an amp that also has a remote bass control knob, which will allow you to "cut" the bass down without fading the speakers. Say the kids are in the truck or grandma is going for a ride and doesn't like the shaking but you all want to listen to some music at a reasonable volume you can just cut the bass with the knob located somewhere up front and carry on your way.
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