How the layout works
Sheet goods are laid out the way a table saw or track saw cuts them: every cut runs edge to edge, so each part comes free with straight rips and crosscuts and no plunge cuts. The calculator places the part that fits a free space most tightly first, then splits what's left along its shorter side, which keeps the offcuts in useful strips. It's the same layout Ripcut draws, and the same numbers.
Boards are simpler. The longest part goes first, and each part goes on the first board with room for it, so the short pieces fill in the ends of boards already started.
Kerf: the wood the blade takes
Every cut turns a strip of wood into sawdust. That strip is the kerf, and a full-kerf table saw blade takes 1/8"; a thin-kerf blade takes about 3/32". Leave it out and a sheet that looked like it held four 12" rips gives you three and a half, because the cuts between them ate 3/8". The calculator leaves one kerf between parts and none at the sheet's factory edges.
If you joint or trim the factory edge first, take that off the sheet size: a 48" × 96" sheet with one edge trimmed is about 47 3/4" wide.
When parts shouldn't turn
Turning a part 90° often fits more on a sheet, but on plywood the face grain turns with it. Cabinet sides, doors and drawer fronts usually need the grain running their length, so they match each other and the doors line up. Uncheck Parts can turn and the calculator keeps every part's length along the sheet's length. For melamine, MDF and shop-grade parts nobody will see, leave it on and buy less plywood.
The sheet's width runs across the drawing and its length runs down. Enter each part's width and length the same way, with the length along the grain.