I have quite a bit of experience with the etcho-matic machine and making stencils, if you guys need any help feel free to contact me. It's a great little unit for the price without all the frills of the $1k machines.
Blagg,
Use the Gator clip. Always take the gun out of the stock, the chemicals you're using for the etching will cause havoc if they run down in the stock, bedding, or are left on the bottom of the bbl from a drip. Tape the stencil onto the barrel and etch for at least 1 minute to gain .003" penetration. You can go up to .01 if you stay on there for 2 minutes. I like to tape the top side of the stencil, etch for 1 minute, wipe the carbon off the stencil with the cleaning solution on a paper towel then etch for 1 more minute.
These results are possible: