I wrote this in the troubleshooting forum, my boss suggested it might belong here too...
Each sphere represents a cube. when you skin using adaptive skinning, zbrush looks at each cube, works out which side of that cube is facing its parent, and joins those 2 closest sides with a poly extrude.
This is why you get overlapping problems with things like hands. think about it; all the finger cubes are pointing towards the same top face in the palm cube of the hand, so they all join to the same face, causing ugly results.
The way zbrush gets around these problems is to subdivde the palm cube. This means there's more individual faces along the top of the palm for each finger cube to attach to, so no overlaps.
This is what the x/y/z-res buttons do, tell the cube how many times to divide in x/y/z to give you enough faces. You can also use the 'ires' slider for a more automated result. Its default value is 6, which means 'as soon as a zsphere has more than 6 children, subdivide it'. So for a hand, you would need this value to be 5, because you have 5 finger children from the palm.
You can be even more precice though. By default zbrush will subdivide cubes equally, giving you a 3x3x3 layout. But you can set these divisions to whatever you like, so the palm cube might have 4 divisions across for the fingers, and 2 down for the thumb (so there's a gap between the fingers and the thumb):
The easiest way to achieve this is using one of the handy zcripts available, like zifedit or zifclick. Personally I prefer zif edit b because it doesn't block the rest of zbrush when its active, but see what you think:
http://www.zbrushcentral.com/zbc/showthread.php?t=8924
Other little tips:
-I find it helps to set the preview mesh density to 1 when layout out the spheres. This way you really see the cubes for what they are, much easier to sort out overlaps and twisting errors this way.
-Because the links are based around closest-matching sides, it helps to keep your spheres as upright as possible. Use the shift-key to snap everything to 90 degree angles when starting out, it makes it easier to visualise how the cubes will orient when skinning.
-The closest-matching sides behavior can be troublesome if you don't watch where you zspheres are in relation to each other. Using the last hand image from above, if the thumb were to be a little higher, the skinning will attach to the upper polygon on the side of the hand. Similarly, if the index finger were further to the left, it would also try to attach to the same polygon. The best way to get used to this is to keep hitting 'a' to toggle between the skin and the zspheres, making small adjustments to the sphere placement. Once you get past halfway, the skin will 'snap' to the next polygon.
Click the thumbnail below for an animated gif showing the snapping behavior.