There is no way you should pay more than a few hundred over invoice for the car, if you are patient and disciplined about the purchase process. Note that even the invoice price does not represent the true cost of the car to the dealer--they get additional discounts and holdbacks based on deal volume.
Your purchase timeframe, "a few months" from now, helps: dealers frequently attempt to gouge (and make no mistake, asking full MSRP is gouging) on newly-introduced models, but this effect wears off quickly (at most, 6 months after launch) on mass-market cars.
The following link offers an excellent recipe for obtaining good prices:
http://www.e46fanatics.com/faq/rizzo.html
The key is to make the deal very straightforward: know exactly what you want in advance, remove any ambiguity about extra charges up front, be prepared to sign immediately if the dealer agrees to your terms, and be equally prepared to walk away at any sign of non-cooperation. The dealer gets a low margin, but in return gets a clean, quickly executed deal.
It's also worth checking whether you or a close family member are entitled to Ford-family discounts, which are sometimes a not-well-advertised part of the benefits packages at large corporations, including many which have no particular relation to the auto industry.