For open water diving, if I wanted to have multiple stages, I would bottom mount 2 stages (with bottom mix) and top mount 2 deco stages. Here's why:
For a long or deep (or both) dive, I'm going to breathe the bottom stages first, even before the mains. As they get lighter, they just float up against the mains, so everything stays in trim. When a stage is empty(ish) I can either throw it (look up what that means if you have to) or it just stays pinned up against the mains until deco time. Next I breathe the mains (steel) which don't get too floaty even when empty and won't be breathed completely anyway because reserve gas. Even if the combination of floaty empty bottom stages under neutralish mains gets a bit positive, I still have the full deco tanks pushing down, and there is always the option to move the mains bottom clip to a lower D ring as would be done if there were no stages at all. Now, when I get to deco, presumably back at the anchor or other up line or near the entry / exit point, I will reach around my left side to get the top mounted 50% bottle on my left side and bottom clip it on the left side. If there was an empty bottom stage still in that spot I can either throw it (up the anchor line or just free), clip it (to the anchor line or whatever) until it's time to ascend, or move it to the top position on the left. Likewise with the 20' stop, I do the same on the right with my 100% bottle and any stage I may still have on that side.
For cave and certain wreck diving, more or less the same, except the 100% gets dropped at 20' and the bottom stages get dropped at 1/3 empty and picked up on the way back to be put back in the same spot they came from. Deco rotation, same (except 100% is already removed from right top). And of course I can't throw a stage in any overhead environment.
