The book Science and Earth History: The Evolution/Creation Controversy addresses that point. It is a large 500 page encyclopedia of Creationist arguments and their rebuttals and I highly recommend it in spite of its price tag.
The argument on the issue of geologic layers being 'out of sequence' is answered there along with illustrations. Basically it has to do with tectonic forces lifting up a segment of the terrain then pushing it sideways on top of the other layers. Further erosion will then produce a cross section where old layers are on top of new layers. It's much easier to understand with the illustrations.
As for the fossilized trees that are vertical (also covered in the book with very telling illustrations) they are basically buried by mud flows from localized heavy flooding. In some areas you find fossilized trees in multiple layers one on top of the other indicating that there was a tendency in that region for massive flooding or volcanic eruptions every so often. These multiple floodings would not correlate with a single flooding event per Genesis.
Again, I highly recommend the book for its comprehensive, detailed and understandable arguments and proofs.