Jay at Indigo Inklings has some great tips for partial cuttlebugging -
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To do this, you kind of have to think backwards. Instead of "blocking" the edges with something, you need to keep pressure from being applied to those areas when the sandwich rolls thru the machine. You can do this by cutting down the acrylic plate and sticking it to the center of the folder with repositionable glue, or substituting anything that is the same thickness as the top plate and positioning it on top of the part of the folder you want to emboss. Or if you need additional shims to make your sandwich work, cut those to size and put them in between the folder and the acrylic plate in the desired spot.
You'll need to run a few samples to be sure you're getting the results you want, but it does work.