In response to a comment on Woot, here is how I separate colors for the print ready file. I'm sure there are far, far better ways of doing it, but this has worked for me so far.
In photoshop I usually end up merging all the layers together.
Then I create a new layer for each color I need and grab the Paint Bucket tool with about 10-15 Tolerance and the All Layers box checked. Next I color pick each color and fill with the bucket into each new layer (the All layers box will allow the new layer to be filled with the selected color based on the color on the original design that you click on). Clicking the bucket tool twice on the same color pushes the color out a few pixels, as does increasing the Tolerance.
Again, this way is far from perfect, can’t handle extremely sharp angles, and takes some finagling on complex designs, but it’s what I’m used to and if anyone knows a better way I would be glad to learn.
I hope this is what you were asking. Photoshop is all I have ever used so I have no idea about any other software.