I do my stencils this way, about 6 different designs on a single stencil. I can't remember off the top of my head what software I used, but it was free and allows me to use 6 individual paste layer gerbers and lay them out.
When I get back to my office I will check the name. For prototypes and pilot runs, it has been an easy way to save money. I can get a full frame stencil and do 6 designs with fine pitch.
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