Barbalee, what is the soil actually like (under the new topsoil, that is) ? When we started our garden at this house, 25 years ago, the soil was quite compacted and "heavy," and didn't drain well at all. Any sort of rain and there would be standing water in the garden. Over the years we've added tons of organic material -- we have a large area of lawn and use a grass catcher, and essentially all of that goes onto the garden for mulch, or else into the compost pile to be used later on, and we even went so far as to work a good bit of sand into the garden to loosen up the soil (disclaimer: although I've read that this isn't necessarily recommended by the "experts," it did work well for us). All of that eventually did get the garden to where there is never any standing water and I no longer use the rototiller.
That said, though, our yard slopes down to the house on one side, which of course means a lot of water drains down and into our crawl space; that problem was helped tremendously by running a French drain along the bottom of the slope.
Since the water is only standing for a day and then eventually draining out, my personal feeling is that your best approach would be to try to break up the deeper layer of your garden spot so the water is able to move on through. And as you continue to garden in that spot, and add compost and such, it should improve over time.
I'm pretty sure there are lots of people here that know more about how to deal with the problem than I do, though... you might try posting on the "Ask a Question" forum to get more input.
