You might consider naming your negative metaballs........"meta-neg#1" or somesuch. This helps with all objects especially when you are dealing with dozens of objects or a complicated wireframe.
For those with very little experience I've found that you can make really cool 'organic' shapes with them but you need to think BIG. In other words, don't be afraid to use hundreds of them to make a really smooth organic shape.

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All the Woes of a World by Jonathan Icknield aka The Bryster

And in my final hours - I would cling rather to the tattooed hand of kindness - than the unblemished hand of hate...