Hi Anna. I had a lot of stomach aches as a kid, too, and my daughter, who is 12, does also. She has acid reflux like you, and she sometimes takes an antacid if it's really bothering her. She has changed what she eats, a little bit, to help with her acidic stomach. Like she won't eat a lot of tomatoes, because they bother her, or spicy food. She also eats smaller meals now than she used to. All of these things are good to do if you have acid reflux.
Because I have an inflammatory bowel disease (Crohn's), my daughter's GI is watching her pretty closely. We think that she will probably have to have a colonoscopy one day to see if her bowel is inflamed, but we're not ready to take that step yet. First we want to make sure that doing such an invasive test is worth it. Not that it's not important to help my daughter's stomach aches to get better, just that we want to balance the risks and inconveniences of the scope against the symptoms she's having. She's already had a scope done of her upper GI (it's called an endoscopy) and the scope was able to confirm that her acid reflux was bothering her esophagus enough to justify her taking a prescript
ion medicine called Dexilant. That helped a lot with her acid reflux; she stopped taking it earlier this spring and has managed to control her reflux pain with diet mostly.
Another thing to realize now that you're 13 is that, assuming you're a girl, your hormonal cycles will affect how your digestive system is working. First of all, you know that you get cramps with your period. These cramps can give you diarrhea. Second, one of the major hormones produced by a menstruating woman is progesterone, and this hormone can slow your bowels down, causing constipation for some people. It can also relax muscles in your stomach, making acid reflux worse during certain parts of the monthly cycle. So it's important to pay attention to your cycle and to understand when things change that it might be related to your hormones. And third, ovulation can sometimes cause pain in your pelvis, way down low by your groin. This isn't bowel pain but sometimes it is confusing to figure out exactly what is hurting. You can use a heating pad on your belly for this and for menstrual cramps and that should help.
Even if you haven't yet had your first period, your hormones are cycling already and are probably affecting your digestive system. This is why I think a lot of girls start having stomach problems when they're 9 or 10 years old, because that's when puberty begins.
I hope this helps you.