This has happened to my baby (now 15 mos old) on a couple of occasions. We were told (and did) exactly what you are doing -- actually, he had diarrhea and vomiting. I think it was the vomiting that was of most concern. We gave him only small amounts of pedialyte for a certain amount of time. Then very slowly introduced small amounts of formula (breastmilk) back to see how he did with it. It lasted about a day. He never got dehydrated.
But yours just has the diarrhea it sounds, then it's not as much of an issue, though I'm betting his tummy is hurting too. I would just continue to offer pedialyte and maybe some bland food (at this age though all they eat is rice cereal). So, you could offer some rice cereal at dinner. Then just offer the pedialyte and normal formula.
I was told that it would take a lot of vomiting and diarrhea to dehydrate a baby. But you are also right that you need to keep giving him stuff to drink! If he keeps having wet diapers, then he isn't dehydrated.
And my 15 mos old baby is a POOP machine. Let me just tell you that YESTERDAY he pooped 7 times - BIG time each time. He's on an antibiotic and must be irritated by it. Anyway, that's just to tell you that sometimes they just poop A LOT in one day!
If your baby is acting okay & not sluggish, having wet diapers, and you can get him to drink pedialyte and his normal formula for meals, then it sounds like you're doing all you can do and I would not think he would get dehydrated. If this continues at this pace, I'd just call your doc back and say, look, he's pooped 15 times today and I just wanted to make sure I'm doing all I can.
I know it can make you nervous. I think that just like us, just keep offering something to drink and remember they are small, so any fluid intake is good.