What works on paper, doesn't always work in the physical world as planned, for a variety of reasons. What follows here are some of the various lessons I have learned while laying out sheet metal projects. Hopefully you can benefit from this guide and save yourself the time I spent learning things the hard way!
Step 1: Sheet Metal Has Thickness
When you're making something out of paper, the thickness of the sheet is negligible--everything will line up and work out most likely in the end. Sheet metal is a different creature in this respect. Bends have radius, sheet has thickness, and tools need space to access a bend. When laying out a simple box with tabs, the tabs will meet the perpendicular face of the next side when folded up to 90 degrees, so when you are folding your tabs, measure in from the edge of the material the length of the tab, plus the radius of the bend, plus the thickness of the material for a perfect corner.
When folding over a seamed edge, the folded-over portion is going to need to clear the adjacent faces on both sides. Slightly notching these helps resolve these issues. A file is sufficient for fine-tuning these bends.
Think of bending sheet metal as what it really is: stretching one face, while shrinking the opposite face in a controlled way.