I use Inventor for modeling for pep because... I guess because I had it after an engineering class!
Anyways, it's very easy to go from inventor to pep, just choose export -> cad format. In the menu, choose STL, and then in the advance menu options I always set it to millimeters (I am not sure it's dire for pepakura, but other 3d stuff like printers can be picky on that and I just do it as a force of habit.
The real trouble is... inventor doesn't always make clean polygons, so you may end up with some stray lines and weird geometry when you unfold the file.