I'm trying to determine population inside Special Flood Hazard Areas. To do this I'm doing a spatial join of census shapefiles with the FEMA National Flood Hazard Layer, using the Boolean field SFHA_TF to identify areas inside the Special Flood Hazard Area. The map shows that the SFHA cuts through tracts, taking pieces of some, all of others. But when I join the two tables, the resulting attribute table contains multiple copies of the entire tract; it does not split the tract into pieces (for example a quarter of the tract if the SFHA occupies 1/4 of the tract). Is there a way in QGIS to do a spatial join between two polygons that will get proportionate shares of the joined polygon? .
There is a plugin which provides markedly different functionality to the stock standard VECTOR | INTERSECTION (or did you use spatial join??) detailed here and available via the standard plugin menu.
Not too sure what your end product is intended to be...