I was also thinking if there was some way you could mount washers into the head and make the eyes to where they could be screwed on........ just a thought  

I want to be able to put them anywhere on the face so I can move around features (have the eyes be really high or really low)

But that's an excellent idea for a puppet where it generally looks the same but has some more minor swapable features.  Like have different sets of eyes for different expressions.  Like a angry eyes set that can be screwed in for scenes where it's upset.

The times that I've seen earth magnets used, they use two of them for each connection.  You do have to make sure you insert them so the polarity is correct on them. I am sure that you could use a washer or something similar but depending on the connection you want it may be you need two earth magnets.

I'm going to experiment a bit with washers because they'd have a lower profile under the fleece.  I have done some tests with magnets on both sides of the fleece and it's worked well, I had to violently shake the puppet far beyond anything that would be done in a show to make it come loose without touching it so I do know it's a great option if the washers don't work.

Daryl,
    What strength are you using mostly?  I was thinking of use these in a hand so that a puppet could hold something.  4lbs, 6lbs what strength and size .25, thickness are the magnets you are using and for which object: hats, glasses etc.  This is the site I'm looking at? http://www.rare-earth-magnets.com/c-9-disc-magnets.aspx

Thanks