Maybe this install wont be so bad... I know that at least in the older model of Prius (01-03) there is a seperate 12V battery in the trunk. The thing is really tiny, and will probably need to be upgraded if it is the same in the newer models. That is what most of the electric system is run off of. Also, the hybrid battery is only used only for driving the car. It might be expensive for her to replace one day, but they are guarenteed to last 100,000 miles. In the old style, they are located under the back seat, and they might make a lot of noise. It would probably be a good idea to take some of that $6K you got refunded, and use it on plenty of deadening material. There is a lot of noise out of the floor on hybrids. Definately invest on sound deadening for the whole car.
A ton of weight will slow the little car down, and definately drop the MPG. I would suggest getting a few of the Focal 13KS mini subs. With the car deadened really well, a few of those should do the trick. It will help you save on space, and she will be able to feel like there is a lot a base if you stick some of those up front.
