I don't quite have the ability to upload pictures, so I hope I can describe this well.
First I recommend that you put the cover on the tefillin first before wrapping, esp. if you have a box that goes encases the entire bayit, not just the square box.
In my description, I refer to the "box" meaning the part containing the parchment, and the "ledge" as the extra part on the sides of the box.
The rosh - Take the knot & push it up to the middle of the underside (white side) of the bayit. Take the 2 ends of the knot "loop" (for fitting around the head) and fold them on the front (black side in front of the box) one on top of the other on the ledge in front of the box. Then wind each strap on each side of the box (Part of the folded loop will hang on each of the sides. The winding will hold the folded loop parts in place.
The yad - Tighten the loop as much as possible until the knot is flush against the side of the bayit. Wrap about half the strap length on the front ledge of the box (black side). Rotate the box to either the right or left (your choice) and wind the rest on the side ledge of the box. Finally tuck any remaining strap under the last wound strap "pile".
I admit, the very last step is somewhat tricky, but it can be done without the yad strap unraveling. You may need to do this a few times until the strap develops its own "fold" so it "knows" it's there (like new shoes, l'havdil. You have to "break them in".)
I hope the written description hasn't confused you. If I can get pics, I'll try to edit this.