First off, I sincerely apologize if this is considered "necro," or if this has been addressed elsewhere in this thread (admittedly, I didn't read every post... there was some argument/drama around page 3 that I skipped past, and I may have missed it), but I wanted to contribute some tips. If you're using Pepakura Designer and using a color printer, you can color the fold lines BEFORE you print, so you don't have to deal with pens at all.
Fourth button from the left, on the second toolbar line... if you hover your mouse cursor over it it says "Set Edge Color Ctrl+E." First, un-check every option except "Mountain," and select a color (I chose red). Then, paint EVERY mountain fold line on the piece. Un-checking the other options is important because it will restrict your coloring selection options to only the mountain folds. Follow the same procedure for valley folds (un-check all except Valley), but choose a different color (I chose blue for valley folds). After that, you may print, score, cut, fold, and glue as normal.
Yes, it's a fairly laborious process, but much less so than coloring with pens and scoring separately. It saved me a good deal of time in the long run. I was doing scoring and marking in the same step because I just couldn't countenance going over the same line twice manually. Originally I began using "micro" point pens (0.5 mm), but I found those to not be precise enough, and finer points were too delicate, and bent under the rigors of scoring. This way I don't have to worry about ruining pens or running out of ink.
A few other tips:
Printing: If you're using this method, increasing the line weight in Pepakura helped me immensely.
Scoring: I'd like to echo that a seam ripper is perfect, but would be better if I could find one with a more ergonomic handle. I know that you can purchase an X-acto blade called a "scoring blade..." Has anyone tried this and found any success? What about other scoring tools? Someone earlier in this thread mentioned "Scor-It." Anyone else have luck there?
Gluing: I've found that a good pair of tweezers and regular old Elmer's white glue make an exceptional combination. Put a little bit of glue on the flap, and then use the tweezers to squeeze the flap to the adjoining piece. This works especially well for longer flaps if you apply a little pressure and slide the tweezers along the attach point. It adheres almost immediately, but can still be reset if it's a little bit off. Eventually I'd like to post a video of this method, which has served me EXTREMELY well.
Good luck to us all!