Clive has the right idea using it.
There's other data files included in the SDK that the make_gsl reads from.
The way I use mine, I added an extra folder in the Terrain SDK, named it original, and keep a safe copy of the global_layer in it.
In the main Terrain SDK folder, I have copys of both the global_layer, and the gsl. When I do any changes to the global_layer, their done to that copy, and saved.
Using the make_gsl is done in that same folder. After making the new gsl, then it's simply copying the global_layer and gsl into CFS3, letting those files overwrite the existing ones.