I would recommend working with a Realtor who is experienced with new construction. That agent can give you guidance on which upgrades are worth having the builder do - hardwood flooring comes to mind - and which ones you may consider handling at a later date.
We negotiate with builders just as we would with a seller of an existing home - understanding price for the area and the type of home that is being built is key. The sales reps in the model work for the builder and are responsible for getting them the best price - be sure to have your agent with you whenever you're speaking with them.
I'm happy to help if you need further assistance - I have worked with most builders in the area and know the process well. You can also visit my site at http://www.topagent.co for more information about me.
All the best,
Brent Rice, Trulia Top Recommended Broker (Pro & VIP)
The Rice Group, Inc.