When I did it before I was converting a site that was "2" columns....actually it was two frames and I wanted the left column to start at the top of the page...the processes was made simpler by the fact the site I was converting was all white background and no borders any where so to get some alignment stuff to work I just used strange but different background colors on each element til I got em where I wanted and then changed everyone back to white....the only thing that was a pain was the footer.....everything in the footer centered to the page so I had to fix its width and shove it over under the center column so that centered elements looked consistent from top to bottom on the page.
I had never thought about Kims idea but I think I might set up a test cart and give that a go to see what I come up with.