The attache case is what you use to carry your stuff (obviously). Along with it, you have a 'temporary' case. This is where you temporarily store stuff while at the attache case screen. What's it for? You can use the temp space to temporarily hold things while you strategically move the stuff in your attache case around to maximize every bit of space. So say you want a rifle but it won't fit. You can first move all your stuff to the temporary case, then fit it in around your rifle in the attache case. Also, the merchant will offer your larger attache cases as the game progresses.

Anyway, I beat the game a few days ago. Needless to say a great game, but with LOTS of replay value.