I currently have a few models I would like to papercraft with decals or logos as separate textures used on a 2D plane floating just about the model itself. Does anyone know how or if it's possible to "merge" these two pieces of geometry in 3DS Max or Blender so that pepakura views them as one and the decal is displayed properly on the model?
If I'm understanding you, it sounds like you're looking to apply those textures (the decals, images, whatever) to the actual pieces so they print in the correct spots in Pepakura? If so, here's a couple of ways to do it.
First one, you would UV unwrap the model in your modeling software, this will give you a 2d template of the model that you then would use in Inkscape/Photoshop/whatever to add your decals to. That then gets plugged back into the modeling software where you can apply it to get your images on the model, and then you can export the model and materials for Pepakura. If it sounds like a lot of work, it is if you are not familiar with how all of that works. There are other ways to do this right from within the modeling software that could work, but once again it will take a bit of youtubing and tutorials to figure it out if you are new to UV work.
Second one, and this might work a lot better for you if you are only adding a few decals on flat surfaces, is to do it right in pepakura. Once you have your base model in Pepakura, scaled and unfolded, you can manually import images, rescale them, and place them manually on the unfolded 2d templates. In Pepakura, you go into (if I remember right)
2D MENU>IMPORT IMAGE, that'll let you get your logo/decal/whatever into the program. After that, you can relocate it and orient parts to make it print where you want it on the paper templates. This is a workaround that won't help you too much ion curved and complex surfaces, but it's a fast way to do something like adding a label to a can of beer/whatever.
These are not the only two ways to do this kind of thing, these are just two that I've personally done.