Ok, to figure out which fold is which, do this...
Open the model in Pepakura Designer (NOT Viewer). On the 2D side (the side where the page layout is shown), right click and select "Edge Color." This will bring up a box. In this box you will see three check boxes, labeled "Cut Line" "Mountain" and "Valley." By default, they will be checked (ignore "Hidden Line"). Uncheck "Cut Line" and "Valley," leaving only "Mountain" checked. Ensure that red is the color selected then go back into the 2D side (don't close this window) and box in all the pages. This will highlight all the mountain folds in the model, turning them red. When that's done, go back into the Edge Color box and deselect "Mountain" and select "Valley." Then, turn the color to blue. Once that's done, go back into the 2D side and box in all the pages again. This will highlight all the valley folds and turn them blue. Then, back in the Edge Color box, click on the "X" to exit.
Now, there is no question as to what is a mountain fold (Red) and what is a valley fold (Blue). When you print these pieces and cut them out and hold them up, print side facing you, the mountain folds will create a peak that will point toward you, and a valley fold will create a peak that will point away from you. How you choose to fold these is up to you. Many use a pen and trace over the lines back and forth to weaken the paper so it folds better. I prefer to score the lines with a dull X-acto blade. If you choose to score with a blade, the best way to do it is to score on the proper side of the paper. A mountain fold is scored ON the red line, a valley fold is scored on the opposite side of the paper from the blue line.
Ok, that's about as comprehensive as I can make it. I really hope that helps.