I'm currently building a custom home and I found the typical price structure for the area I'm building in as:
Cost = time & materials consumed or used in construction plus consumables, insurance, engineering costs, shipping costs, permits and a few other fees.
Adm Overhead - 4% of cost
Supervision - 4% of cost
Profit - 10% of the sum of above.
Some builders charge a "fee" that runs 10-20% instead of breaking it into the 3 components. I found and am using a builder who builds the house on a combined fixed bid for the foundation and structure plus allowances for things like appliances, flooring, cabinets, etc.
Under the "cost plus" system, the owner gets to review/approve hundreds of pages of invoices, timesheets, etc monthly.
Of course, there is room to negotiate and there are variations of the above theme. The above is for Texas Hill Country area.
The architects fee is in addition and separate from the above.
FWIW-I considered being my own general contractor but rejected it as I felt my inexperience in construction and knowledge of the local market for subcontractors was poor and that I might wind up spending more even if I saved on the builders fees, not all of which go away if you DIY. I talked to a few people who considered DIY in the area, and they told me that most of the best subcontractors high balled their bids as they did not wish to work with amateurs and they had more work than they could handle anyway.
I did not talk to many banks re. DIY, but the ones I did were reluctant to supply financing.
One person I talked to had a real horror story. He went DIY, at first, and luckily for him stopped before he wasted too much money. Turns out, his foundation crew failed to follow the drawings and he wound up with one that had the wrong dimensions and the in slab plumbing was incorrect plus some other flaws. At this point, he turned it over to a established contractor. The lawsuit is now in its second year.
DS