John Woodmorappe's Studies in Flood Geology is an excellent discussion of this issue. For the example you use, during the flood of Noah, flowering plants would tend not to fossilize. They would be buried in layers as the flood waters subsided after floating for days in mats of vegetation. Fossilization does not occur today except under very special conditions where the specimen is buried quickly and under conditions where the bones are replaced by minerals. Fossils in these layers correspond to the very base of evolution, but they certainly do not fit the pattern of the oldest layers being on the bottom.
Evolutionary theory suffers from a similar problem.
Most creationists have abandoned the idea of the water vapor canopy as the source for the waters of the Flood of Noah. Instead, they favor the idea that most of the flood waters originated from subterranean sources. The mechanics of keeping all the water in orbit proved to be too problematic. Now that does not mean that a canopy didn't exist, but it did not exist to the extent previously believed. Within young-earth creationist thinking, there are different schools of thought that have different perspectives, and the fact that we do not agree on all things just points out our mortality and lack of omniscience.