I would encourage you to carefully look at existing homes first. A custom home will not only cost more, it will cost a LOT more and when it's time to sell, won't bring the added cost back to you.
If you must build, find a builder with a portfolio of plans that you can move little things here and there. Using an existing plan is going to save you a boat ton of money.
My son is a structural engineer, so I hear about the process from him on buildings in general. First the architect works with you to design the house. Then when you're set, they send it to a structural engineering firm who goes through it and comments on the things that defy physics and sends it back to the architect. When a plan is close, a shop drawing is then drawn up by the architect. That's sent to the structural engineer who points out all the mistakes, code violations and more defying physics things that have to be fixed. Finally, when everything is good, signed off and stamped, the plans are sent to the contractor and as the senior guys at the structural engineering firm say "The contractor does whatever the hell he wants", ignoring all the proper ways to do things because he thinks he knows better. I doubt the structural engineer makes visits while the build is being done, but for bigger builds, my son has visited sites with senior engineers who show up, smash dry wall to see joints, find they were improperly done and let the contractor know that they have to pull major things apart and do it right.
What's all this cost? A hell of a lot more than a cookie cutter design and more still than an existing house. I won't say twice as much as an existing house, although that's possible.