If your coordinate system is not in the list you can't add it using MGE.
But, if your data is SHP data, uploading the files to the server as SHP will use the associated WKT string in the .prj file. If you upload and convert it to SDF it should also retain the WKT string. If you add the SHP/SDF to a new map it should detect the WKT from the data and use that even though it isn't in your list. That will be fine if you don't have any raster images. The raster images would require a Spatial Context Override and your entry won't exist. You would either have to use an image format that includes the WKT such as GeoTiff or ECW (and possibly mrSID).
I'm not completely sure on this, but if you have a copy of Map 3D 2009 they have a feature to add coordinate systems. You would then have to copy the modified Mentor libraries to the server (and any Studio machine that needs it.
Regards,
Dave