Hello,
There's quite a bit more about this on a post i submitted on the Lulzbot forum here
https://forum.lulzbot.com/viewtopic.php ... 201#p40201
Basically, I found it was better to set the G-code offsets in S3D and live with the offset preview (set it back to zero when I wanted to see the real preview).
Setting the starting gcode M218 commands made the machine do weird things. I believe what the Cura slicer does that come with the lulzbot, is it take the offset value from the machine setup, and adds it to each move command in the gcode for the print. that's why you don't see a M218 command in the Cura starting gcode.
I ended up returning the S3D software and just use Cura that came with the printer. It does what I need without too much fuss and I didn't have enough time to take advantage of the S3D features.
Hope that helps.