For the box layout, start by measuring the object you wish to box. Mine's a round coaster so all sides of the base will be of equal length. Next establish how high the walls need to be. The more challenging part is figuring out the flaps and slots. When measuring for flaps it is crucial to allow extra material length for bend allowance. (There is a whole world of materials engineering around bend allowance...) I added extra length in narrowest part of the flap, where it fit the slot, for bend allowance. Any excess is easily cut with scissors.
I drew my box outline using Illustrator. The prototype was cut out of a flattened wine box. (Free, recycled materials are my fav.)
When folding the test, I used a red pen to mark file alterations.
Fold the bottom flaps first. Use a straight edge and the back of scissors to compress the cardboard where you want your folds. This helps override the corrugation and give a nice straight fold.
Next, put the straight edge inside the box, this shows the alignment of the box top flap fold. A mistake I made was folding the front lid flap at the same time. The front lid flap fold should be moved towards the center. (See how the flap wants to crumple rather than slide in nicely?) A little scissor modification and it's OK.
I would recommend adding very lightly etched lines to show where folds should align. Happy box making!