It always pays to keep an eye on costs when building a custom home. Here are just a few key points from a larger article at eplans.com

Don't overbuild for the neighborhood. A home that is better and bigger than any other in its area will not command a fair price at resale. Instead, the assessment will be colored by the lower-priced homes around it.
Monitor construction allowances as the home is being built to ensure you're getting what you asked for (and are paying for). This includes decorative details as well as structural elements. If you and your builder agreed, for instance, that a particular brand of insulation would be installed, don't accept a lesser brand — at least not without a cost adjustment.
Use only a certified general contractor. The experience of a well-qualified contractor is invaluable to the home-building process. In addition, seasoned professionals have established relationships with suppliers and subcontractors — something you cannot possibly hope to get without years of experience in the business.