Hi Chris,
Just an opinion, but not my, about using sandpaper. In Russia lives a master Nikolay Korshenin. Of course, I can provide link to Youtube seminar about grinding and honing of woodworking tools
http://www.youtube.com/playlist?list=PL2CC67F5C668CED14
but there are 4 parts, each - near one hour and in Russian only.
So, Nikolay is very experienced person, speaks well Japan and triyed a lot of differents Japanese waterstones, natural and man made.
He is very well known in Russian speaking knife community due to practical knowledges and recommendations.
Upon Nikolay, if you have soft waterstones, sandpaper flatening will be enough good. But if you have any kinds of hard waterstones, in above mentioned link he spoke about Shaptons, effect of flatening with carbide powder will be better.
When on flatten with carbide powder we have (let's imagine) three hard layers
1) waterstone
2) carbide powder
3) lapping plate or glass
with water of course
And flattening goes enough smoothly because all three layers are hard.
When we flatten with sandpaper we have FOUR layers - three hard and one soft, and this soft layer goes like a rubber
1) waterstone
2) carbide powder glued to a sheet of paper
3) glue + paper of sandpaper
4) lapping plate or glass
In this system the layer consists from glue + paper is a soft, like rubber, and grains of carbide powder make a little jumps down when we press to sandpaper by waterstone and high when we take of waterstone.
This is, upon Nikolay, is not good for hard waterstones.
Second negative.
When on flatten waterstone with free carbide powder on a lapping plate or glass at the first all carbide powder grains are the same size. When the flattening progresses all these graines become disrupted and smaller and smaller. But this happens with the most part of abrasive we using to flattening and we have a smooth action of abrasive, but without clogging.
When on latten waterstone with a sandpaper, some abrasive grains stay glued to the paper, become dull but not disrupt. The quantity of free carbide grains are smaller so we have a less of action - bigger time to flatten and more clogged sandpaper sheets.
But this, upon Nikolay, valid for hard stones only.
Probably this hard to read with my English, but I did the best of my.
Regards,
Georg.