I think you need to let go a bit and not worry about controlling the campaign as much as
3e and
4e assume. In a megadungeon sandbox, it is not the GM's job to ensure balanced encounters or wealth-by-level. Skillful or lucky play should get the PCs over-standard wealth, for instance (traditional XP-for-gold ensured that poor PCs were not high level, but gold didn't translate to magic items - I'm really talking about item wealth, here). Monsters should, on average, possess average wealth, but insert plenty of variation - either use random tables or pseudo-random distribution.
Edit: It's very important though that if you are assigning treasure, you MUST do it before the monster is defeated. You absolutely must not be ticking off treasure packets in a pre-determined order.
Always remember that the players have a great deal of choice how deep they wish to delve - they set their own risk/reward ratio. This means you need lots of stairs to lower levels; it is NOT sandbox design to have just 1 way down, only findable after defeating the Level Boss. Don't worry if after going up to say 4th level they still insist on seeking out all the easy 1st level encounters -
don't convert these into level-appropriate challenges. Easy victories mean less XP and slow advancement. If the players don't like it, there are those stairs downward...
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