Wolfinlied
When Pepakura unfolds a model, it will make a lot of small pieces if the model has not been optimized for a paper model. However, I haven't learned how to do that yet, so anything I unfold is many pieces also.
However, if you right click in the unfold window, you will see a select called something like Join Adjacent Pieces. If you place your mouse over an edge, and a red line appears, it is telling you there is a piece that can be joined. An arrow at the midway point will show which direction the part will travel. Be careful...if you select an edge on a large piece and the arrow is pointing towards the smaller pieces, when you left click, the large part will move to the location of the small part. Since this might cover other parts, it isn't desirable, and since there is no Undo (at least none I can find), it's difficult to recover without restarting the entire process over.
Main thing is you would be better off learning to use a 3d program, and designing a model with one of those programs which is compatible with a paper model. There are numerous threads on the forums which go into that, including a PDF tutorial on building an aircraft in Rhino 3D, one of the better, but more expensive modeling programs. Metasequoia is a bit easier to learn and there are some tutorials on the net for learning its use.
I have tried them, but since I am a tired, old man who can't learn new tricks, I stick to designing my models by just drawing them with a CAD program.
Good luck. There is a lot to learn when it comes to producing card models. But I saw a few people who built some of my models, and it felt good. 8v)