wow, This is a pretty major issue. If, in fact the builder DOES know what he is doing, then he is probably a little cheesed at you right now, not a good way to get a project started. But it is really his responsibility to be able to communicate with you how the house will be sited and what the finish foundation elevations and site grades will be. Who is responsible for the design of the house? Did the builder provide the plan or did you hire an architect. You need to be able to communicate with your builder about these things. If he can't describe to you how the house will end up looking in relation to the finish grade then you maybe should hire an architect to review the plans and site and communicate your wishes to your builder.
Some basic issues that need to be addressed: - Any construction like this requires footing and foundation inspections to detect any gross deficiencies. - Foundation needs to bear on undisturbed soil, never on fill. - Site drainage issues should influence location and design/drain details.
These issues are too important to trust to how well you learn some basics from some web site somewhere. Every site has its challenges, some more than others. You need someone that is experienced in these matters to help make these decisions. It is quite likely that your builder knows what he is doing, but you need to communicate better with him or find someone that can help you with this.