I am searching for the easiest solution to intersect a polygon Featurelayer with another polygon of given geometry (IGeometry).
With the ITopologicalOperator I managed already to get a list of intersecting polygons and I can calculate areas and area percentages but when I wanted to write them back to the Featurelayer I realized that I do not have the polygon parts situated outside my selecting polygon. I attach a small jpeg explaining what I want.
So if my understanding is correct, you want split the polygons in the layer with the given polygon. let's call it cutting polygon. As you said, you can get the polygon parts inside the cutting polygon using ITopologicalOperator.Intersect method. In order to get the parts outside the cutting polygon, you need to call ITopologicalOpearator.Difference. See the link below.