How to keep the cost down.
"Before I begin the whole process, I thought it might be a good idea to ask you contractors what do I need to know to be a good customer? What will make me a pleasure to deal with, and not one of those clients that make you roll your eyes and trade annoying customer stories with your colleagues?"
1. If possible, don't go with a contractor that requires a big deposit before any work begins. It will make you nervous, agitated and frustrated and you'll take it out on the contractor.
2. Make all your decisions on plumbing and lighting fixtures, trim, flooring, etc.... ahead of time and don't make a lot of changes throughout the project.
3. Understand that working in the "field" (i.e. your house) is not like working in an office. A schedule is a guideline but things happen. You will need to be flexible if the HVAC guy has an existing customer who's furnace just went out and he needs to delay your project to get heat back up in their house.
4. If one spouse is going to be the "go to" person for the contractor - keep it that way. You would not believe how many times spouses have had different desires/requests on a project.
5. This last thing is a really good idea for big projects and I really like it. Schedule a weekly meeting (even if just a half hour) where you will meet with the general contractor. This will set aside a specific time where all items that need to be discussed will be discussed when everyone has the necessary paperwork.
"What can I do to insure that I get a good deal without compromising workmanship? By that I mean, not how do I make it cheaper, but how can I insure that I am getting value. When the bids come in, what should be the deciding factors in making my choice?"
I lumped these together as my response may answer all of them for you.
1. First of all the best way to keep your finished-job cost down is to not go with the cheapest bid. Go with the contractor who has the best references and a reputation for everything in writing up front and no surprises.
2. Second, like Grumpy said - watch the extras. I saw that you're adding a bath room and a powder room - don't go nuts on the plumbing fixtures or the tile. Don't go nuts on flooring and lighting (natural and electrical). Windows: go with good windows in factory stock sizes. If you have to get custom-made windows the cost will double/triple.
"What kinds of things can be considered negotiable?"
The business of contracting is such that a contractor is unable to change materials costs and labor rates. If there is anything to negotiate, it's lower-cost materials or items that are cheaper to install or doing some of the work (like painting) yourself.
"Any BS indicators to watch out for?"
Don't believe the "If he has a new truck, he's gonna cheat you" advice you may hear. Many contractors wear out trucks fast so it's common for them to have new ones to replace the relatively new ones that they are wearing out.
Now just one of my opinions but I always tell people to watch out for demand for large amounts of the money up front (Note: this is a recommendation for general contractors only, some other contractors, like window replacement for example, may require a larger deposit - this is not unreasonable). For the first month we're going to be tearing up your house and you'll want to make sure we're paid so the work keeps going....

Seriously though - contractors should have credit accounts. Our policy is that we only ask for $1000 for a project to secure the date and set up dumpsters, etc.... We have credit accounts and if it takes us more than 30 days to get to the first payout, we're doing something wrong.
Hope this helps Ian. If you need more help, don't be afraid to ask. I go through about 20 of these projects a year - a homeowner only goes through it once or twice a lifetime. It's perfectly fine to ask these kinds of questions.
Tim