This is a classic example of why you want a licensed architect with construction administration services.
Step One: You need a program. Working with a licensed architect, they will go through your house with you and create a detailed list of work to be performed. Then they will prioritize this work by what must be done, what would be nice if done, and what must be done before another, etc.
Step Two: Set a budget. Many people think this is step one, but without knowing what you must do and what you can do without, you cannot set a realistic budget. The architect can also assist by providing sq/ft costs, average costs or actually helping you get bids.
At this point, you will have a rough idea of what this project is going to cost you. I'll also point out that your house may qualify for Historic Rehabilitative Tax Credits. Since you are planning on renting the property (income producing) there are Federal credits as well as State ones; if this is followed correclty, and the forms done well you can get more than 20% of your costs (including design, engineering & archtiecture services) back. You will need an architect and/or Tax advisor familiar with the program-it takes work, but here in VA you can get 45% of your costs back in credits-20% fed, 25% state; and the credits can be syndicated (sold) if you don't / can't use them over the next 20 years. (Don't do it by yourself; you won't get through the hoops and pitfalls.)
Step Three is to hire a General Contractor. Again your architect will prepare the drawings and designs to clearly explain what repairs and new work is to be done. This can be provided to contractors and they can bid the work. The Architect can also arrainge for Phase work, so you can keep your budget, etc. The Architect can also prepare bank proposal documents that will show the work needed, the suggested repairs and a cost anaylsis with repayment schedule that you can use to secure a construction loan.
The Architect will also have access to common AIA documents and contracts that spell out exactly how the contractor will perform. So the contract will be clear, common and protect both you and the G/C.
Step Four is the answer to your question. If the Architect has construction administration services; they will oversee the construction, arrange for keys and access to the building, arrange for securing the building (either through the G/C or themselves), etc. They will also be insuring the work is done correctly. You will just have to live with a messy (dust, torn down areas, etc) home for awhile if you plan to stay during construction. You can even designate start and stop times in the contract so no work occurs before you leave or after you return home. You will just come home and see halted work progress until it is done.
Step Five (or Four B), all invoices will be sent to the Architect: they will confirm the work on the invoice is complete, the items ordered are on the job site, etc. The architect will then recommend you pay all, partial or none of the invoice based upon their review. You only write the checks for what the architect says to. The builder deals with the archtiect, you deal with the architect. The architect ensures you get want you wanted and are paying for. They also will place liens for the sub-contractors to ensure they are paid and are not able to comeback later and ask for additional costs or claim the G/C didn't pay them.
The cost for this architectural service varies and can be a per-project percent or hourly. The fee is easily made up in peace-of-mind, you not having to worry about quality or costs, and in design improvements that you or the builder may not have considered. Plus, if you do go for the Tax Credits, all design fees are elligible in how much you will get back.
My firm does work in NY; we have a current project in Rochester. But we do not have staff to do construction supervision in NY (we are based in VA). But if you want more info on the Tax Credits or help with doing the programming and design, we can get you started, and even help you interveiw a local architect for the construction administration portions.
Best of luck on your project-it seems a fun one!
Source: http://www.herlonginc.com