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I began using Tamiya weather master and loved the effect but I find that it wears off with use and handling... I have read that some pigments and such should be sealed with varnish. Would a matte varnish work to seal these effects in? Will a matte varnish also matte out the metallics and the like? What about a satin varnish (though I am not exactly sure what effect satin is going for)?

Matte varnish would seal your pigments/weathering, it will also matte your metallics.

Satin varnish is essentially a semi-gloss.

If you want to retain the metallic shine on your paints, I would suggest looking for a pigment fixer, you can use plain old alcohol, but MIG and AKInteractive also make an acrylic based one from memory.