Don't over think this, it's really simple.
Create the models in xLights exactly how you will physically build the model. If you have a string of lights and you plug node #1 into the upper left corner of your mega-thingy, then xLights should have the mega-thingy defined as starting in the upper left corner. All models are controller independent. I'm switching controllers this year and no configuration changes will be done to my models other that perhaps new channel assignments.
A common issue is scrolling text is backwards. That is always because the pixels are plugged in backwards from the way the model was defined.