For a start the article that you have linked to is so badly written and ill-educated that I would dismiss it almost immediately - but I'll give him the benfit of the doubt and do it scientifically.
The layers cannot be different ages - well that's speculative at best and almost certainly wrong as his reasoning that all strata are formed by floods is entirely misinformed.
Organic matter does not need to be fossilised to be preserved, lack of oxygen can do the same thing even in a wet environment.
How can a tree be found upside down traversing several strata? I don't trust the validity of any of the assertions in the article but let's suppose it's true.
A tree blows over due to a storm and falls into a stagnant lake. This lake has high concentrations of sulphur, methane and CO2 but no oxygen. The tree will float for a while and become waterlogged at which point it will sink to the bottom of the lake and lodge upside down. It can remain in this submerged state for a long period of time without decomposing even if it isn't buried (the Mary Rose is an example) while events above the surface of the lake cause layers of sediment to be deposit gradually building the lakebed up and over the tree.
Now it's sealed and won't decompose even if the lake ceases to be. Over time the fossilisation process will preserve it for evermore and the result is a fossilised, inverted tree.
Like I say, I don't trust Dr. Kent Hovind's scientific reasoning, sources or objectivity so he may well have elevated a rare event into something that can be found everywhere. Maybe he would offer his sources so that the trees can be carbon dated to see if they all died at the same time regardless of where they were in the world.
I suspect he won't but that would help him to prove his great flood theory.