So, now that we've looked where your theory leaves you in reference to a few things concerning the Flood, let's look at where OUR position leaves US. Let's assume for a moment that the Hydroplate theory is correct, and the canopy theory is wrong.
Because we said that there are two firmaments, one being the crust of the earth, the other being the firmament of the sky, it leaves us with an accurate location for where "the deep" of Genesis 1:2 is, below the crust of the earth, as Psalm 33:7 says, the deep is in storehouses beneath the surface of the earth. According to the Hydroplate theory, those storehouses are simply many large interconnected chambers of water beneath the crust of the earth that were formed on Day 3 of the creation week. These chambers are the source of the water for the fountains of the deep.
This is consistent with many of the verses that use "the deep" or "depth," such as Genesis 49:25, Job 38:16,30, Psalm 33:7, 71:20, 104:5-9, Proverbs 3:19-20 (which uses the same word as in Genesis 7:11, "broken up"), 8:22-31, and Ezekiel 31 (the entire chapter, but specifically verses 4 and 15).
So if the firmament called Heaven (not "of the heavens") was instead the continental crust of the earth, then what about the firmament "of the heavens"? Well, as we have said before, that does, just as your position does, refer to the sky, just like "windows of heaven" refers to rain falling from the sky.
So how does the "windows of heaven" phrase fit in?
As I mentioned before, but will do so again here, if we take the order in which Genesis 7:11 describes the events of the flood happening to be the actual order, then we can assume that when the fountains broke forth, the windows of heaven were the resulting rains from the fountains, just like if you go to a public square and there's a fountain, the water goes up, and because of gravity, comes back down again, but it's usually dispersed from the more solid stream that it was on it's way upwards.
If the hydroplate theory is accurate, it solves both the problem of where the flood waters originated, below the crust of the earth, which means there's no requirement for miracles in either supernaturally removing heat due to there being too much water in the atmosphere (boiling all life on earth) OR supernaturally transporting water to above the earth to cause it to rain upon it.
And that's just for where the water comes from.
What about where the water went? What happened to all of the water (a bit less than half of all the water on the earth since creation, if the crust divided the waters of Genesis 1:6 exactly in half) that was below the crust of the earth?
Well, let's start by taking a look at the reason God placed Adam in the garden:
Then the Lord God took the man and put him in the garden of Eden
to tend and keep it. - Genesis 2:15
http://www.biblegateway.com/passage/?search=Genesis2:15&version=NKJV
What happens when you don't tend a garden? It becomes overgrown, yes? Weeds, overgrown plants, and specifically, if there's a good source of water nearby, a tree's roots will grow, and as a result, you get a really, really big tree.
Some of the following is conjecture, but can be supported by scripture. Allow me to tell you a story that I hope you'll read.
Imagine such a tree, in the Garden of Eden, that has grown large because of the source of water it sits on, so large that its boughs stretch from mountain-top to mountain-top, we're talking a GINORMOUS tree. The source of water this tree was above was constantly pumping out water, enough that it formed a huge river that went out of the garden, and then split up into four smaller rivers, each of which went out and watered the whole earth, so much water that it's no wonder that the tree above it grew so bit.
Now, when God kicked Adam and Eve out of the garden, the garden no longer had anyone to tend to it and keep it, and so you can imagine that a few centuries later, and the entire garden would have been completely overgrown. So this tree that sat on the source of the river, its roots grew so thick that it eventually choked off the source of the large river, causing all of the rivers to dry up, resulting in a world-wide drought. And so, as time went on, the descendents of Adam and Eve, and Cain and Seth and their wives, started to resent this "God" that had kicked their ancestors out of what was supposed to be a paradise, and blamed the drought on God, accusing Him of drying up their source of water (typical humans, amirite?), and so they form a search party to go look for the source of water, so that they can restore their water supply.
So they follow the riverbeds upstream, and come across this giant tree, the base of which is in some mountains, and is surrounded by trees which are large, but come nowhere near the size of the giant tree.
These men, they think to themselves, "this must be this so-called "God's" garden, we can see the remains of a giant river at the base of this tree, yet no water is flowing. Let's cut the tree down, so that the water will flow again, so that we may drink."
So they cut the tree down. Its branches fell on the mountains and the valleys, its boughs laid broken by all the rivers of the land, and the ground shook with the sound of it's fall, and when it fell, the fountains of the great deep broke forth.
God was laughing at them, saying, "You want water? Here, I'll give you water. I'll give you so much water you'll be comforted by it." And so the entire earth was flooded.
This storyline (the parts that matter, at least) can be found in Ezekiel 31.
So, you might be wondering, what in the world does a tree in the Garden have to do with the Flood?
Well, let's compare two verses, for a moment:
The Tree of the Knowledge of Good and Evil:
So when the woman saw that the tree was good for food, that it was pleasant to the eyes, and a tree desirable to make one wise, she took of its fruit and ate. She also gave to her husband with her, and he ate. - Genesis 3:6
http://www.biblegateway.com/passage/?search=Genesis3:6&version=NKJV
The Tree in the Garden of Eden:
Indeed Assyria was a cedar in Lebanon, With fine branches that shaded the forest, And of high stature; And its top was among the thick boughs.The waters made it grow; Underground waters gave it height, With their rivers running around the place where it was planted, And sent out rivulets to all the trees of the field.‘Therefore its height was exalted above all the trees of the field; Its boughs were multiplied, And its branches became long because of the abundance of water, As it sent them out.All the birds of the heavens made their nests in its boughs; Under its branches all the beasts of the field brought forth their young; And in its shadow all great nations made their home.‘Thus it was beautiful in greatness and in the length of its branches, Because its roots reached to abundant waters.The cedars in the garden of God could not hide it; The fir trees were not like its boughs, And the chestnut trees were not like its branches; No tree in the garden of God was like it in beauty.I made it beautiful with a multitude of branches, So that all the trees of Eden envied it, That were in the garden of God.’ - Ezekiel 31:3-9
http://www.biblegateway.com/passage/?search=Ezekiel31:3-9&version=NKJV
Long story short, we can reasonably argue that the tree that was cut down was the Tree of the Knowledge of Good and Evil (from here on out referred to as simply, "the Tree"), and that the Tree was placed on top of a natural spring of water.
So... again, what does this have to do with the flood, and particularly, the Hydroplate theory?
More on that later, this post is long enough as it is, and there's plenty to talk about in it currently.