[Stiglr]

Not sure how well the "knife" tool will work on a 3D object (haven't played with it much).

But, with such simple objects as these, the "long hand" method might be worth a look.

1) Select the roof surface (top) in Surface/wireframe mode. Subdivide the surface a few times.
2) In Vertice mode, arrange the vertices nearest the middle of the surface to align with the "square" in the center formed by the chimney object. Use your viewports to make sure your vertices stay "flush" with the slope of the roof in the side views; that is, don't create any bulges or distortions in the roof.
3) Select unused subdivided areas and merge them to "clean up". The idea is to have only "one square surface inside the square" surface of the roof.
4) Now that you have the shape of the chimney, eliminate that separate chimney object, and instead extract it from the square surface you've formed in the roof. If it's necessary for texturing reasons or whatever, you can always select the surfaces that form the new chimney and create a new object from it.