You will not be told what color you can paint your house or what can be done inside your house. You can change the windows in your home although if you have historic wood frame windows often times the most economical choice is to restore rather than to replace those windows.
If you want to demolish your home or significantly alter the exterior characteristics of your home or build a new structure your plans would go through a review called a “Certificate of Appropriateness” (COA) by the Historic Landmark Board. Normal maintenance and repair are exempt from COA review. The goal of the COA review is to maintain neighborhood character by discouraging and/or preventing the sort of changes that over time can erode what makes a neighborhood special.
The City's COA review criteria are specified in the City's preservation ordinance and the city considers the guidelines of the National Register in their COA review.