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I don't think you can do it in Distiller. It sounds like you'd have to go back to the original document and converge the colors there. I wonder if you could open the EPS in Illustrator and create the colors there. I'm not familiar with "ArcGIS", but see if you can converge there first.
Also check the EPS' are they vector or raster separations? Haven't used PLTS but when I was looking intro setting overprints with Arc I found the only way was with PLTS but this generated raster files for the plates. If they are raster you may be able to combine in Photoshop with an action without any degradation.
One thing to keep in mind layering these separations is what happens when a tint overlays a solid ink or vice versa?
But I'm pretty sure you should be able to output the tints on the same fileWe have a meeting with ESRI's PLTS product manager tomorrow so while I won't be able to go into depth I'll run it past him.
Also I wouldn't recommend Illustrator due to the complexity of maps that are usually output via this method and also the fact some postscript objects sometimes go a bit haywire when opened into Illustrator and these are often things not immediately apparent.
I was able to get the color separation from ArcMap. ArcMap uses a color management interface called "See Spot Color". By modifying the support file (SCS), it is possible to place multiple ink percentages on to the same plate.