This has come up before, trying searching for "running D" on this board.
As for your problem specifically, I'm not sure if I can suggest anything for running a marathon. But for general running/working out I'll give some advice. First, I would take the acacia both at night and in the morning before running, to try and prevent the D. You should probably increase the amount of acacia you are getting, but slowly. Don't run on a full or empty stomach, and don't drink too much water, this may cause more D.
"I thought when you exercised, your bowel system was supposed to turn off, but mine turns on full force."
Nope, opposite. When you exercise a lot, it stimulates your muscles in your abdomen, which in turn can stimulate bowel movements. People with IBS-C are encouraged to exercise a lot in order to relieve their symptoms. People with IBS-D, tend to have a hard time doing moderate or heavy exercise.
Also I suggest doing ab-workouts (if you aren't already) to help condition your stomach muscles and get them used to lots of tweaking and pulling (from running).
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Kat
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Re: Stomach problems when running - help!
