The only problem with VFFs is that sometimes after 2 hours of running the balls of my feet start to hurt. Here is the solution I used to keep the balls of feet pain free for 20 miles of running last week.
Last Wednesday I decided to head out for a 20 mile run. I have not ran in shoes other than Vibram Fivefingers since October and didn’t want to go back to my other shoes if I could help it. For this you need the Komodosport version of the Fivefingers. Carefully remove the Komodosport insole. It is glued down near the ball of the shoe, be careful not to rip it out, just slowly work the glue away from the insole. Once you get it out, position the ball of foot cushion just behind the metatarsal heads. You don’t want the cushions to sit directly under the metatarsal heads, but rather just behind them. This actually helps to encourage toe splay.
You can see a video on how to position the metatarsal pads below.