I have IBS and a sensitive stomach, so I have unfortunately had many vacations affected by GI issues. These problems run in my family, so we have the advantage of knowing where the nearest restroom is at all times while in WDW (we're getting there with DL :lol
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Anyway, I have taken both Pepto and Immodium, and I can say that for just an upset stomach, Pepto works great (whether it's nausea or acid/indigestion). Dramamine is not only effective for motion sickness, but for nausea and vomiting as well (I always have a couple doses of all of these on hand when in the parks....it pays to be prepared!).
For, um, bathroom issues, Pepto really doesn't help me (if you are having both an upset stomach and the other, you can take both; however, my pharmacist said not to take them at the same time and recommended taking them an hour apart...I recommend checking with your doctor or pharmacist before combining meds).
In October, my aunt brought the new Immodium chewables. They were amazing and really saved the day! They worked within about 15 minutes for me, and I didn't need a second dose. Plus, you don't need water, which is a plus. They have now become a must-pack item for every trip. Also, I find that keeping mint Lifesavers or other mint candies can soothe an upset stomach, although it can make acid worse.
I also find that the combination of intense sun and heat (plus not drinking enough) can cause stomach upset. I'm careful to drink at least 8oz of something every hour, and I am so careful about balancing being outdoors with being inside in the A/C.
This may sound like a bit much, but there have been many trips where days have been ruined because of GI ailments. Bringing the right meds and taking precautions (like the great tips others have mentioned) can really minimize any inconvenience or suffering.