Hi Bagel and welcome to the community
First off I want to start by agreeing with the guys advice on how to proceed with your build. The pep files work fine for resin and body filler as you get to apply the filler for a smooth finish. How ever for foam they make your piece far to bumpy and give unnecessary ridges that are easily avoided. Like Mike said if a piece can be made as one then do so. If you check my Ironman thread then you will find a tutorial by James AKA Xrobots on how to use pep files for foam. Not all pieces need his technique but some benefit from it and its up to you which techniques to use for each template. I did my helmet in 2-3 days as I didn't have unnecessary cutting to do.
Some of my advice.
1. If you can keep your templates as one piece then do so. Don't cut out the foam as you would the paper. You have realised this now so hopefully you can steer away from it, even if it means losing what you have marked out already (foam will always be wasted).
2. When building your piece (helmet), I would recommend never marking out and cutting all your pieces in one go. I only mark out and cut one piece at a time. Then before marking and cutting the next hold my card/paper template up against the foam piece to make sure it works/fits. Then if it doesn't you can always alter your template accordingly. For paper it always works but due to heating and bending foam it stretches or expands the piece slightly so alterations are pretty much always needed. Better to alter your template than have to remake or try to recut the foam. Of course save the templates from one side of the helmet so you can flip them to mirror for the other side.
3. Buy the pepakura password. Then when you alter the pep files to suit foam you can save it and not have to reunfold a piece as I used to have to. You will thank your self for the expense
Its a shame I don't have more time at the moment as I want to do a tutorial on how to unfold pep files to suit foam builds. Maybe after new year I will do one as I know it could make all the difference to some people on their builds. I know I could just unfold it for them but then I would have a constant string of requests for unfolding. By knowing how to do it yourself you get a better feel for the piece even before you start to make it so its beneficial to know how to do it. I am not promising anything but I will try to find the time to do it.
If you have any questions feel free to ask as I am always happy to help. Ask on your thread as I will subscribe so I know when you have (I get instant emails letting me know and pretty much answer straight away).
All the best,
Tom.