I think a lot of issues can be solved when it comes to unfolding in pepakura, Mesh resolution is unimportant as long as you model with good edge loops. Simply altering your fold angle in pepakura will make the program view you edgeloops as long strips, they also make it easier to manually cut your model,
I think its best to avoid triangles because when you're modelling with subdivision surfaces/hypernurbs/whatever your application calls it, your tris interfere with nice smooth loops.
As for boolean operators, I very rarely use them at all, and I cant think of a time I've had to model something where using a boolean was necessary