In regional and urban planning such as in design actions they are usually involved different themes and disciplines; especially when the goal is to improve, restore and re-functionalize existing minor settlements in rural-urban context. For this reason it is necessary to define integrated methodologies able to face inter-scalar issues and interdisciplinary themes. Authors propose a framework for a decision support system based on the treatment of geographical data and on the integration of the data sets that have dissimilar origin, diverse formats (they may be not only digital) and different meaning value. This complete data set refers to various disciplines and it is possible to deduce specific knowledge throughout analytical passages and assessment steps. In the paper authors describe: a methodological approach to support planning activities; the technical support to seek a (dynamic) balance between urban density and rural fragmentation; a Best Practices database to support scenarios in rural-urban context. Authors first expose the application field, than the logical framework of the whole process, then describe some related spatial analysis applications and finally they introduce comprehensive case study of the whole procedure.