As you will eventually need a building permit and as the Alton Building Inspector is the person who will interpret the zoning regulations and codes, you should make an appointment with him to go over your general plan.
http://alton.nh.gov/CodeEnforcement.asp
Bring info on the existing cottage and septic system and simply have a preliminary discussion about what you want to do. While we can all speculate, that is the only way to get a real answer.