To change the bounding box threshold, hit 'd' for Display options and look about halfway down the panel. I generally keep it to around 500,000 polys on my machine (P4 3Gig/1Gig Ram 7800GT Video Card), but you'll need to experiment on your machine to get the best results.
As for the boolean operations, unfortunately they can be less than reliable on many occasions. It's a sad fact that you should always save your objects before trying the operation because they can (and often do) cause LW to crash.
There are a number of things you can try to make life a little more reliable. First, try segmenting your main box - maybe try two or three slices horizontally through it, and one vertically. This give LW an easier time in calculating the new mesh. You might also need to try doing your subtractions in smaller quantities - really there's no real guidelines on this - just shifting the geometry slightly might even work in some instances...
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