Arrange your flies in pattern or rows which looks presentable to you and you are happy with the look & layout.
Take measurement of layout. This will give you inside dimensions of box. Now you can determine the size of the box for that layout. This layout will enable you to make box correct dimensions, thus will save you from adding or subtracting subject matter.
An ole fly reel or ole advertising or a fishing snapshot (of you or person getting gift) or ole fly tying vice along with your flies would be a good touch. You know, something related to fly fishing or fly tying or personal picture. A small creek stone painted on- Penns Creek & date, Kettle Creek & date you made box or your name & date instead of creek name.
Box I would make corners at 45 degrees. Maybe use some reclaimed wood. Maybe non-glare glass.