It sounds like you want a GIS. That's what we use for managing real world geographic data.

http://www.cartographersguild.com/tu...using-gis.html

GIS software is, of necessity, fairly complex, and there's a bit of underlying theory (The basics of spherical geometry and projections) you need to understand if you are going to pull this off.

Simply put, no one projection of a sphere to a flat map will be able to cover the whole surface of that sphere without distorting something. The map is flat, the sphere is not, and so something has to give. You can have a projecion that preserves angles or areas over the globe, or one that preserves both, along with distances, but only in a small area. So you need to use multiple projections, and that requires being able to convert between them, and knowing which ones to use for a particular task.

A GIS will allow you to maintain layers of "raw data" rather than graphics, and that data will be geooded so the software knows exactly where it is. It allows you to style that information to get graphics, and combine it and analyze it (combine temerature and precipiation to get climate zones for instance). It can also convert between projections.