having diarrhea due to amoxicillin is a very common and known side effect.
it happens in approx 5% cases. i would advise you to take the medicine preferably after taking your meals and further you can take curd or buttermilk for few days till the medicine is on.
Next Steps
in case if the problem still persists please visit your doctor who has prescribed you the medicine. he would either chenge the medicine or tell you to take prebiotics that will counter the side effect of amoxicillin.