I am guessing you are going into a planned community and are dealing with a home builder, and not a 'contractor'. This is often the case that the charges given to you are extremely high and it is something which you can go in hard on. A typical rate may be between $60 and $90 per speaker run. Maybe less, maybe a bit more, but not much more. Unless you are in a very high dollar area and in an extravagant home, then I would negotiate hard on those numbers. Because at $900 you may be better off talking to A/V companies or even a decent electrician who may be able to wire the entire theater and then you can repair the drywall and repaint for less.
I would typically charge about $250 in materials (or so) and about $300 in labor to prewire a unfinished home theater space to a projector and a local equipment rack location. Conduit would be a bit more. So, about half of what you are being quoted and I'm in the DC Metro area which is not an inexpensive place to be.
If I were you, I would nail them down on a per-wire charge, or find out how much ONE Ethernet drop is, and how much ONE pair of speakers is. If you do go with a 'under the screen' equipment location then you can get by with just a piece of conduit run to the projector (don't have them run ANY wires!), have an Ethernet jack put near your equipment rack, and then have power at the projector and power at the equipment rack. You can ask for a 'dedicated circuit' which they will sometimes do at a fair price.
In my experience, many of these guys don't know what they are doing and are making a money grab with significantly overpriced cabling and very high labor rates. They will wire for speakers in your ceiling in a theater which is very bad IMO. They won't consult with you and talk about what you want and where things ought to go. They won't talk about treating the room at all, or how lighting should be placed in the room for best results. So, I lean towards perhaps having them do the most minimal job possible and tell them it is due to their ridiculous rates. You can even tell the builder that you absolutely refuse to let them gouge you with such things and will recommend others avoid them as well while such a pricey company is being used.
You may find that they offer a slight bit of leeway. You may also ask if they have multiple companies they use for this type of wiring and work because you feel that the company they are recommending is ridiculously overpriced. You may even want to call a local A/V company to see how much they would charge for a prewire job in a open frame home. Go in with those numbers.
I would say the same thing with your flat panel television locations - They only need to run conduit from the equipment location to the TV location and put power at both places.
You will need the 'multimedia' drop at the equipment locations. That's usually 2 RG6 cables and 2 cat-6 cables. Insist upon cat-6!
Since you are new at this, the tendency is for companies to take advantage, but if you go in with a requirements list and a budget, and put pressure on them to meet your budget instead of them trying to charge you a flat rate, then you have a certain right to make a fuss.
I did the better part of an entire home as a retrofit with a dozen zones of audio and multiple video drops with added networking keypads, and speakers throughout with 5 guys in a single day. About a ten hour day - so 50 hours or so. We went through thousands of feet of wiring, but I want to say that the total was about $4,000-$5,000 for that level of effort as a RETROFIT! If the walls were open we would have been done with the work in half the time or less. A good $1,000 of cabling would never change, but the labor would have been $2,000 or less I would expect.
Just some numbers to consider and some thoughts.
Hey - do you have floor plans you can post or you can link to?