Actually, just figured out my own issue, even though I had the universes set correctly, the channels were set in xlights for 300 each but there were only 50 strands, once I set the channels to 150 it worked
BUT....
As of now the megatree's universe 1 is at the 9 o'clock position (middle left) with universe 6 at the 6 and universe 12 at the 3 o'clock position. When looking at the house preview, it's showing strand 1 at the 12 o'clock position (middle back) and going counter-clockwise from there.
I told xlights that the starting location was bottom left, but how do I tell it exactly where to start and go counter-clockwise from there?