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Off course, you have to start at the eave of your roof with your shingles and lay out your chalk lines parallel to your eave and work your way to the ridge.
Any un-squareness will have to be taken into consideration at the ridge, when you put the ridge caps shingles on.
Your chalk lines will be square with the your starting point, the eave, and will be square to each other all the way up to the ridge.
The only part that will not be square is your last chalk line relative to your roof ridge.
You really just need keep the horizontal chalk lines parallel to your eave and the trim the edges as you go.
I guess I do not know the actual extent of the roof not being square, can you give me an idea?
Ok, let me know. No hurry.
Let me know when you come back online.