However, if you look at the oceans today, yes, they're all connected, but in three main bodies: the Pacific, the Atlantic, and the Indian. When God says, "Let us gather the waters into one place," it was probably in one huge body with a single continent of low-laying land, or Pangaea.
Then, if one imagined that between the plates and the lower layers of the earth (about five miles deep) was a huge body of water, circling the globe under the ground/water. That water would be very hot and under pressure, allowing it to reach around 250 degrees F. Then, by some activity (earthquake, comet, meteor, etc.), a huge crack appeared in Pangaea. This water would suddenly de-pressurize turning into steam and shooting out into the atmosphere, causing vast clouds to encircle the earth and start raining (for the first time in history).
Soon, the water would come out as water, quickly widening the crack via erosion. The land underneath the thinning water layer would be under lots of pressure, so when the crack widened enough, it would 'jump' out in a large mound, sending the two well-lubricated 'plates' away from each other and run into the same force on the other side of the globe, making the land buckle into mountains and rebound away, making a large gap of water in between.
After a probably short period, the water would run out, and the land would settle onto the earth again, but the now-huge clouds of vapor would still be raining millions of gallons of water on the earth. After another period (40 days?), it might stop, leaving the earth covered in water. It would probably be cold, from the 40 days of no sun through the globe. Maybe causing an ice-age.