I always be sure to NOT lay threads on top of each other when winding on my warping reel. That would be asking for tension issues.
You can push the warps against the back of your board as you wind, but keep them laying next to each other, don't wind on top of existing threads.
When I am tying my CROSS after finishing winding on a section, I make 4 ties. I use white shoelaces on the top threads on each side of the cross, and dark shoelaces on the bottom threads on each side of the cross. When I need to wind more than one section (which happens frequently) I label each section #1, #2 etc. Because the top of each section is tied with white shoelaces, I can't get them upside down etc. on my lease sticks.
When I'm all done measuring, I just thread my lease sticks on either side of the tied crosses.