Saving in MM is simple. Your progress is saved whenever you play the Song of Time, but a lot of what you've done is not. Basically you keep important things--bosses defeated, masks, weapons, songs learned, money that you have deposited to the bank in West Clock Town. You cannot really save mid-dungeon, or mid-anything for that matter, or you have to start it all over. It's do or die. You can make a save file at an owl statue and everything you've done that three-day cycle is kept, but time isn't reset. Some players can go through the game all in one three-day cycle (after the mandatory one where you're a Deku and can't do anything about it). I'm not one of those people.
Yep. Boxes. I can't wait to see what ours looks like. Or maybe I can. Given the premise of the game I can't be sure. The Japanese boxes all suck though. Books and covers, of course, but they don't do the games justice at all. Sometimes less is a good less--the MOTHER series has always had plain red boxes in Japan, which are strangely hypnotic as if to say "We'll just let this game speak for itself." You could say the same about the Japanese M&L boxes except for that they have just a tap too much for that. Superstar Saga and Partners in Time, on the other hand, have really impressive boxes that fit the games like gloves. Looking at them makes me want to play the games. That's good advertising right there.