First and most emphatically, do it right the first time! I strongly discourage you from going generic to start and later ripping things out and replacing them. This is counter to everything that green building and sustainable construction are about?it will cost you more money and it will be a huge waste of resources.
I expect that you'll be surprised at what you accomplish with some careful research and a positive "can do" attitude. Your first step is to talk to your designer as soon as possible to set your priorities. This will give the designer a head start in selecting the best possibilities for you, so that you have plenty of time to review the options. You?ll also want to talk to your builder and find out what green and sustainable products and finishes he and his subcontractors are familiar with and what their incremental costs may be. For all but the most progressive professionals, green products are new and require a learning curve to fully understand and implement. This is typical of sustainable construction in general: Expect to spend more time in design and planning to get everything worked out before you go into the field and start swinging hammers. The more thorough you are in your homework, the better and more cost-effective your final result will be.
Unless your builder is already part of the solution (we'll keep our fingers crossed!) you may be limited to green finishes rather than really integrating sustainability into the project. Because the project is already under way, it is likely that the builder has already contracted for or even installed things like the heating and cooling system, water heater, windows, insulation, and so on. The good news is that in terms of indoor air quality, the finishes you choose for your floor and walls will have the biggest impact. GreenHomeGuide has many articles on green flooring, paints and finishes, kitchens, and bathrooms. For more ideas, check out other green living magazines and websites. Even some of the more traditional design and architecture magazines are featuring interesting ways to integrate new green products into the home.