Some builders will negotiate on upgrades, some will not. We're in a bit of a Seller's market these days, so negotiating discounts may be more of a challenge than it would have been two years ago. Builder upgrades can be broken into two categories: 1 - Construction Upgrades, 2 - Interior/Design Center Upgrades. In general, builders make a good portion of their profit on a new home off of construction upgrades, and most of that is made on design center upgrades. Accordingly, you may find them more open to negotiating on design center upgrades than on construction upgrades.
You may also want to consider another approach. If you have the funds available for use after closing on the purchase of your new home, you may want to have the upgrades done yourself after closing. You may find better deals by sourcing materials and labor yourself, rather than paying the builder to do the upgrades. This is often the case with flooring and countertops. You would also avoid financing those upgrades over 30 years.
I would also recommend you have a Buyer's Agent represent you in any real estate purchase transaction, including new construction. Remember, the builder's sales representative does not work for you and has no obligation to protect your interests. In fact, the opposite is true in that the builders sales representative works exclusively for the builder and likely earns less commission if they give you discounts. Accordingly, they will probably be reluctant to go to the mat for you to get a discount. A Buyer's agent has a legal and ethical duty to protect you best interests. They work for you, not the builder. And keep in mind, it costs you nothing to have a Buyer's Agent, as the Builder pays the commission to the Buyer's Agent. Lastly, make sure you have your Buyer's Agent with you the first time you visit a builder. Some builders will not allow you to introduce a Buyer's Agent into the negotiating process after the fact.
Hope that helps. Please let me know if I can answer any more questions for you. For example, another way to save money with a new builder has to do with mortgage options (whether they have an in-house lender, or whether they are willing to pay some closing costs). I'm happy to discuss that with you if you're interested. I'm not a lender, but as an experienced Realtor, I am very familiar with that process.