As Alli K said, the BRAT diet works well. That's what I would do when my kids went through these spells. He must have some kind of virus or something and will probably recover in a few days. I would watch his temperature and pay close attention to fluids. If he stops drinking fluids, take him in right away. Kids dehydrate at a rapid rate. This is the time to give him extra water (no gatorade...it can stimulate loose stools due to the glucose level, or sugar, and the salt may cause him to retain water, but pedialite is safe). Also, the acidophilus in the yogurt is very healthy for our normal flora in our gut. If he eats this just about everyday it might help with the odor and could help with the soft stools. If he's got a normal temp, is acting fine, and is keeping fluids down, I would only worry if this continued for more than a week. And remember, no juice or sugar products this week..........
Maybe try waking him up at night to go potty. I would also make sure that during the day he would take frequent visits to the restroom. It would be helpful to lay a pad underneath him for the time being when he goes to bed, too.
It's not fun, I know, but it's normal and will pass......it sounds like you have a healthy little guy who rarely gets sick. With this being a new experience for you, that says a lot. Keep up the good work!
Good luck!