There are different types of loans available for custom home builders construction. Discuss them with your lender to determine which is best for you.
A Construction Loan usually carries a higher rate of interest and has a specific time frame in which the job must be completed. At that time you would move to a permanent loan.
A Convertible loan is a Construction loan that rolls over into a Permanent loan and is then converted to a Mortgage. You save some of the closing costs by having this type of arrangement in place.