On the website is says "The starting area is the most important in any installation. If we're looking at a single room, the biggest concern is how square you are in that area. However, if the installation goes into other areas and your starting line is out of square to these areas you'll find yourself correcting as you go along. This is why we recommend a control line."

So how do you correct (for glu downs) if you in the middle of the room or ??? (I will not be using any door thresholds to hide any corrections)

I would start at the longest shot possible going thru each room or hallway , get that starting line as square as you can and work both ways by splining.