I'm doing a research project trying to determine how the planning phase of building early houses was done. Did the builders have plans done and would show them to prospective clients for them to choose from? Or did each builder design each house to meet the needs of the home owner? Any information would be really appreciated. Are there books that cover this?

I think that you will need to be more specific about the time period that you are looking for. For example, Abbott Lowell Cummings has an excellent book about the early timber frames of Massachusetts which will give you considerably information for 1625 - 1725. There is also a good site at the fine arts department of Boston College.