You're not actually supposed to save. The makers of this level knew that it would crash the game and couldn't be loaded because it was too big. As for the order, I remember at one point there were a series of tubes into warps which were designed so the last one you entered would warp you out, regardless of the order.

However, I would strongly suggest you simply don't play QoB. It's frustrating, the gameplay is awful, and (in my opinion) the tileset isn't even that good.