Sounds to me like you have all the tools you need to start, and I would start with a prototype, you will get some practice in and you will make something, and you will not fuss about making it perfect because hey, it's a prototype. You will learn a lot about how to make a box and you an apply that to making a better one and then an even better one, trust me no one makes a perfect anything the first time around.
NO ONE!!
For your compartment I can think of many things to do, for example a false bottom that you hold in with magnets. If you have a pivot point and you know that if you push on the right side of the bottom that side goes down, freeing the false bottom from the magnets so you can remove it. If it is just for cash you could have a false top in your lid, similar idea, or a pull out piece of trim like a tray in the lid or the bottom, lots of idea.
My point is to make a basic box, don't worry about the corner joints just yet, make it a butt joint, make a box with a lid, a lid that just sets on top is fine, make your box then experiment with ways to make a false bottom or such, have fun, prototype to your hearts content, then when you have your idea worked out in cheap plywood or cheap pine or such, then buy some good wood and make a nice box.
YMMV