Funny you should ask! I just saw an episode of the Scrapping show on the DIY network that talked about this.
They made their own stamps by using the punch with a foam insole (like Dr Sholl's) instead of paper. She was using a balloon shape from Sizzix. After you get the shape, peel off the back & stick to a clear stamping block. You could use anything, but that's what she used. I've never seen them, but WOW! Much better than the wooden things I have as you can see right through them to position the stamp properly.
If you're afraid you'll get Versamark on the edges of whatever you stuck the shape onto & thus on your page, you can cut extras & layer them to make the shape stand off the base better.
If you have a punch that won't hold the foam insoles....you could also punch the shape, emboss that & then stick the embossed shape to your page. I have a pair of medical tweezers (not eyebrow type) that I use to hold the paper. (I've also used it to remove wrong stitches from my counted cross stitch.) You can rub the Versamark on the punched shape, pour on the powder & heat while holding with the tweezers. Then fill in the spot where the tweezers were with your embossing pen if you have one, or just repeat the process on the part that got missed.
You could also just punch stencil material, lay the stencil on your page & use the pen to color in the shape.
If you don't have a pen, think about getting one. They're great for filling it messed up spots as well as freehand stuff. Do you have a 000 paintbrush? That's what I use to brush off excess powder that's hanging off the edge of my shape.
Oh - another idea I just read but can't use myself. To cut down on the static & therefore excess powder on your paper, wipe the paper with a dryer sheet before you start. It sounds like it would work, but I'm allergic to the scent in the dumb things.
Good luck & let us know how you make out!