You've gotten me thinking, so I'm going to write a Hub about fleas. (It will take me a little bit to research & write it.) For now, let me just say that I've used both Frontline & Advantage products and they are both good. I would NOT use any "over-the-counter" products you could buy at Walmart or other stores. My personal preference is to use both chemical (prescribed by a Vet) AND natural ways to eliminate fleas.
The downside to a cat that's become used to the outside is they have the freedom to go to the "bathroom" where-ever they want. Outside, this is not a problem...it's when they come inside, they might not remember the "rules" about using the litter box. I'd suggest you gently remind him to use the litter box by lightly tapping his nose when you catch him "squatting" and hopefully BEFORE he actually goes. Then, as calmly as possible, put him in his litter box. The idea here is to give him as much positive reinforcement to use his litterbox inside.
If you're overly concerned about leaving him outside all night when you're "away", then you might want to consider bringing him inside. If he doesn't respond to my suggestion above on positive reinforcement, then you might want to consider putting him in a cat enclosure (cage) overnight. Make sure he has food, fresh water & a small litterbox. This would then allow you to know he won't go outside the litterbox, but I don't advise using the enclosure for an extended period of time.
Hope this helps.