In my opinion, You can't do it!
If your parts are cut good and square and you have nice tight glue joints, that is as good as it gets.
You can "help" the joints hide by sanding the outer surfaces after assembly nice and smooth before finishing. And you can help it further by sanding the end grain of the parts to a higher grit of sandpaper so that any stain or finish will take the color closer the color of the face grain. But, if you are butt gluing a box, you will be able to see any joints that are made.
If you are using miter joints and get a bit of a gap in the corners, you can try filling them with either glue or shellac mixed with sawdust but, it will still be noticeable. If you have fairly tight corners with just a small line of gap, you can run the round shank of a screwdriver down along the corner pressing the wood fibers tighter together before finishing the wood and that is about as close as you are going to get!
I make a LOT of boxes and in most cases, I use miter joints and try to get the wood grain to match up all around the sides as close as I can but, still if you look closely, you can see where I might have patched a gap or two.
Rog
PS, I'll try to post a picture of a box or two.