I also own the 6600, 7700 Horizon, MC10001, MC11000, so I have had a good bit of 'practice'.
If you are using Janome pre-wound bobbins, you probably should not attempt to use it down to the last inch, because they are wound on a heavy duty bobbin winder, and this usually causes some overlap at the inside of the spool. The overlap actually causes the bobbin to hang up inside the bobbin case - so try to watch and stop the machine before it gets too close to the center.
If you are using other brands of pre-wound bobbins, you should rewind them onto Janome bobbins because the commercial prewound bobbins (even the plastic ones) are smaller than the Janome bobbins and have been known to damage the machine.
If you are winding your own Janome bobbins, you need to do what the other person said; put the thread through the hole in the top, hold it while the winder spins 3 or 4 times, then stop it and cut the tail and then start the winder again. I have never had a bobbin that I wound like this hang on me.
Good luck.