The best way to do it is to use rubber boots.
Get a pair of old rubber boots. Cut them down to size (optional). Wear them and pour fresh urine into them, just enough to cover the whole toe. Soak for a few hours. Tie some towels on the mouth of the boots, this will prevent spill when walking around. The fungus should be gone in a few days.
I did this for 6 hours straight, for 3 days, using old urine. Fresh urine will work as well. My toe fungus never came back (that was 2 years ago or so). I've had it for years.