I've copied the 'triton' sub folder and renamed it 'tritonbeta'.
I've opened 'tritonbeta' in the sub editor and moved one of the generator room bilge pumps to the reactor room by altering its coordinates.
I've saved this new layout.
I've changed sub_folder to 'tritonbeta' in game options.
I've tried running sub commander and at the end of the loading bar I get the 'Illegal Memory Address' box.
Damn it.