Maybe you are using the .pdf files and not the .pdo
If you are using the PDF, you have no way to see the 3d model of the piece you just printed.
If you are using the .pdo, which opens with pepakura, I don't see where your problem is.
And for the 45°/90°, you actually have to guess and see where you feel to do one.
If you see an angle on the 3D model, then you have to cut it on the foam to make it accurate.
I would suggest you to read JFCustom's excellent thread full of nice tips for foam building first
I actually cut it in 2 pieces to fit in. It's fits me perfectly but I did had some troubles to get in when it was a one piece. I used straps and buckles to connect the cod back.
If you guys want, I can show you more in depth how I did it.