Typically B. Subtilis is well tolerated at low doses, I myself took B. Subtilis for over 4 months with no side effects. However, B. Subtilis is a soil organism and not native to the digestive tract. It will eventually die off by itself in a matter of days/weeks. Also anti-microbials such as oil of oregano, GSE, and garlic will likely kill it as well.
B. Subtilis is NOT B. coagulans.
If you think you're dying, go to the hospital.
I would give S. Boulardii serious consideration if you have chronic diarrhea and/or Candida.
Also, who told you enemas were bad for intestinal flora? Not true, your intestinal flora recovers pretty well in these situations. Chronic diarrhea is probably way worse on your beneficials then an enema would be.