Assuming you have two finished floors, a basement, and an attic...
Running wires retrofit for wall boxes in the first floor is usually pretty easy - you cut a hole in the drywall, drill a hole from the basement up, run the wires through
Running wires retrofit for wall boxes in the second floor is usually pretty easy - you cut a hole in the drywall, drill a hole from the attic down, run the wires through
The problem is this: how do you connect the attic to the basement? The stuff you have to drill through to make that run -- first floor up to subfloor, and second floor down to subfloor, is covered up once drywall goes up. Also, finding an unobstructed path from attic to basement is tough as it is, and tougher once drywall's up and you don't know what might be buried in those walls (many pipes and wires snake around horizontally, for example). So if you can get those two connected before drywall goes up, life's MUCH easier.
A conduit pipe is basically just a plain old plastic pipe -- though it will be colored grey or blue instead of white so that your inspectors don't confuse it for water or sewage pipes. If you can get your builder to run a pipe -- preferably 1" or 2" diameter -- straight from your basement to your attic, you're set. Once you're in the house, you can just drop some cat5 cables down that pipe from the attic to the basement. In a pinch, a pipe connection is a pipe connection, but that pipe being smooth and straight will make it MUCH easier to get wire down it. If they have to elbow the pipe, it's going to be tough to pull wire through and the amount of wire you will actually be able to pull through will decrease greatly.
A co-worker of mine was able to pay his builder to run a conduit pipe from attic to basement. They ran it in the heating plenum -- this will almost always be the place to do it. They put an elbow in his, which made life painful when pulling cable, but it's still way easier than not having conduit. I was able to get in my house before drywall got up and have my foreman "not see things," so I ran a few pipes straight up my plenum. The sales people are always a pain about this kind of stuff and their opinions basically don't matter anyway. Chat with your foreman and you might be able to get in there before drywall goes up -- all depends on whether he's cool or not. In general, you will find that making friends with the foreman is an all around good thing.
Note that for inspections, the pipe must be capped on both ends, otherwise it's considered a fire hazard (hot gas can shoot up from the basement). Once you move in, uncap and shove wires down, and you can stuff some rock wool or other insulation in the ends when you're done to get an air seal.
Centex - a friend moved into a home with an extensive pre-settlement punch list, some of the things were serious problems (I forget what off hand). They get to settlement day and not a thing was fixed, and they basically told him take it or leave it. He said that they did actually fix some things, but it took them about six months. One thing in particular he mentioned was that his bedroom and master bath wasn't insulated right underneath (on top of the garage), so the floors were freezing on winter mornings. A lot of what he didn't like about them was just their attitude and way of dealing with customers. Also, according to my mother, they were recently featured on some or other investigative TV show for ignoring problems (20/20, 60 Minutes, etc.).
In some fairness, I had plenty of unfixed punch list items on my house closing day, but most were fixed in a week or two afterwards. I think some of that just goes with the territory. Also, when I started my homebuying search, I asked my agent -- long time friend of the family and really good agent -- what builders were good and which weren't. Her answer: They pretty much all suck, they all cut corners. Later slightly amended, as I learned that really, it's the foreman who builds your house, and the foreman who controls whether you get a good house or a lousy one. The problem is that you contract with a builder and don't get to meet the foreman before it was too late. I had a mediocre builder but a great foreman, and the result wasn't excellent, but it was pretty good. With a different foreman, though, I could have had a lot worse experience.
Warranty: 10 years from now, cat5 is going to be a novelty. And I believe you'll find that if they weren't competent enough to do it right the first time, they aren't going to be competent enough to understand the problem and fix it -- and vice versa -- if done right the first time, you just won't need the warranty. I am a little surprised by this statement though and suggest you dig in if you were going to go there. Most folks I know who had wiring done by the builder had that covered as a one year bumper-to-bumper warranty item, but not on the longer warranty, which is typically only for structural/MAJOR stuff. I smell a sales critter who's not being fully truthful.
I did BTW meet the "Verizon" home wiring folks when they were out working on a neighbor's house. (it's actually a subcontractor to Verizon subcontracting to the builder... joy) I talked wiring with those guys for a few minutes just for kicks, and the whole conversation confirmed everything I thought those guys would be. I was glad I didn't pay them my good money.