Although the pattern may repeat across the fabric, the repeats are not identical. When I make stack n whacks I buy 6 or 8 repeats. I cut the fabric in half length-wise and then cut the repeats cross-wise (from selvage to selvage).
Those are the sections I line up very carefully. I actually hand baste the obvious points of the pattern together. I can then cut my shapes and the basting keeps each bunch together until I'm ready to work on it.