As fas as it comes to my body, here is my story. When I was a marathoner and lifted just the bare minimum I was at my heaviest, that includes higher body fat. When I stopped marathoning and running all together and started to focus on weights/pilates, weight went down together with body fat.
I think big part of it was the lack of controlling appetite and carb intake -- I was always hungry -- plus using some muscles for fuel as well during those long runs.
Nowadays I started again with more cardio, and guess what, weight is climbing up together with fat and appetite.
For me, less cardio, controlled carb amount and more weights/pilates is the trick.