gerbtool merging design
Ok, well if you can read them all in with GC-Prevue (graphicode.com), you can have each board on a seperate set of layers and then just align them to how you would like them to be.
The hard bit is that your manufacturer would then need to be able to read .GWK files (graphicode format).
Otherwise you would need to be getting a demo version of GC-CAM or even CAM350 etc and doing this and exporting rs274-X Gerber files.
Or on the other hand you could always just send them all to your manufacturer and tell them to do this, its so easy that they will usualy be able to do it no problem. most proberally better than yourself if you are not used to doing it. Ask them.
Roland.