You might have to use something, like Illustrator or Freehand, to break up the SVGs, and save them off seperately. Honestly, it's not worth the hassle, unless you have a VERY good reason (for instance, the $600 Klik-n-cuts can cut much thicker material).
So you're going to have to experiment with, and find suitable converters, virtual printers, etc., or else do like other non-CraftROBO users have done where they export into some format and import into different software. Basically you're just asking for extra hoops to jump through, because Pepakura Viewer doesn't support them directly. You are experiencing the exact reasons why I do not recommend any future readers buy non-CraftROBOs. You went out on a limb by deliberately buying unsupported equipment, and you'll probably have to be the one to figure out how to fix it, and then tell US how so that future users will know. As for your problem, sorry, I don't have much to offer.
