For the hand plates all I did was cut out the circles and the middle piece and then glue them a little more in. Here is a picture to help understand:
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As for tips, I can suggest to really study the 3d model that pepakura shows you and to also compare that to reference images from the game. For the folds, all I did was follow the lines that the template provided. But keep in mind that pepakura was meant for paper, not foam, so sometimes you have to be the judge to see if the cut is worth it or not.