For the Atoma you would want the 140x : http://www.chefknivestogo.com/at14dipl.html
I believe the Atomas have a better distribution for their diamonds so their plates leave more desirable scratch patterns on a knife edge when compared to the DMT stones. I don't think that will matter much for flattening other stones though.
The DMT Extra Extra Coarse (I think also around 140 grit) : http://www.chefknivestogo.com/dmtextracoarse.html
DMT is known for being good quality and reasonably priced. If used for knife repair, I don't really know if the scratch pattern is as big a deal at this low of a grit. They are all gonna scratch the crap outta the knife. lol Higher grits are where I think it might matter most, but I could be wrong. Again, not a big deal when flattening.
The DMT Dia Flat lapping stone : http://www.chefknivestogo.com/dmtxxcexla.html
This one is meant for flattening with a super flat surface. It can also be used for blade repair as well, but it might be overkill unless you want your stone as flat as it can possibly get.
This one is a generic 140 grit diamond plate that can be used as well : http://www.chefknivestogo.com/140grdistflp.html
It might not be quite the same level of flatness of the DMTs or Atomas, but it is just fine for flattening stones. It's not like it will be u-shaped or corrugated or warped or anything. lol It's just that if you tested the flatness with equipment, the DMTs and Atomas would probably win.
Finally the Shapton Glass Diamond Lapping plate : http://www.chefknivestogo.com/shdilapl.html
Diamonds embedded in extremely flat float glass with a tolerance of 5 microns in either direction. Pretty much the flattest surface to flatten stones with and a price tag to match. You can buy it if you want to, but something at this level is not needed at all unless you are extremely, uncontrollably, and belligerently anal.
Personally, I would go with either the $30 140 grit generic or the DMT XXC as a step up in quality for stone flattening. Any more than that and (in my opinion!) it's a waste of money for something you wouldn't see a difference in.