A row of holes can look straight on each loose board and still refuse to line up when the box goes together. One easy mistake is measuring from the top edge on one part and the bottom edge on the next. If the boards differ slightly in width, those marks describe different lines.
Choose a straight edge on each part that will share the same position in the assembled box, such as the bottom of a side. Check it with a reliable straightedge first. A bowed or ragged edge is a poor starting point; correct it, or choose a sound reference that suits the design, before laying out the work.
Make a light pencil mark identifying that edge and the intended inside face. Keep the marks where they can be removed or will be hidden. Lay the parts out as they will sit in the box, including any left- and right-handed pieces. The reference marks should make sense in that arrangement, not just when every board faces the same way on the bench.
Measure each related hole centre or groove location from the marked edge. If using a marking gauge, keep its fence against that same edge and test the setting on scrap first. For several matching parts, keep one proven setting rather than resetting it from a ruler for every board. Reference the marked face consistently when the depth or face orientation matters too.
Before drilling or cutting, dry-assemble the parts and compare the marks across the corners. Hold the actual hardware in place if it is available. This catches a reversed part while the fix is still an eraser. A shared reference keeps the layout consistent, but it cannot correct badly sized parts or a box that is out of square.
Practical takeaway: pick the reference, mark it and use it for every related measurement. Leave those pencil cues in place until the layout has passed a dry fit. One deliberate starting edge is easier to trust than a fresh guess on every part.
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