'tis quite complicated, and I think you can only really learn by watching (or at least seeing pictures of the process. But I'll try and explain briefly.
Hold it up and shake it out, check the inner pantleg seems and make they're folding to the side which makes it lay flat. Lay it down, with the back side up. Straighten the legs so the the seems line up on the sides. Grab the top of the hakama, pull it forward and gently flip it over so as not to lose your progress. Begin finding/lining up pleats from the middle of the hakama out. Once everything is straight and neat, you'll notice the pantlegs are about three inches wider than the back-board at the top. Fold each pantleg inward so that the sides are completely straight with the back board. Now, fold the hakama in thirds from the bottom up (if the back board sticks out, fold it in too). It should now be a nice flat rectangle. Fold the long ties in thirds or quarters and lay them in an 'X' on the hakama. Take the short ties and loop them one at a time around the 'X' (this part must really be shown.) Fold up remainder of short ties and tuck under the loops to hold them in place.
Now after all of that, I suggest you find someone who can show you properly!