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Here is a very good link showing how to create x3g files using Slic3r.

http://www.3duniverse.org/2014/01/05/using-slic3r-with-a-flashforge-creator/

Here is a video showing how this is done....

When adding a glass plate, is it necessary to do some other settings to account for the loss of the added Z height? Or is there a sensor in the extruder module that will sense this?