Meditation is about bringing the energy from the brain down into the gut to help the gut do it's job right. There is no such thing as success, failure or doing it right. The whole point is to stand back and let the brain rest. Thoughts will interrupt your meditation - that's ok. Simply watch the thoughts as if from a distance. Let thoughts float away if they will and if not, just let them float. You are not trying to succeed, the benefit is simply in the trying.
Meditation can be hard work - don't expect it to bring you bliss. What if 6 minutes per day of this hard work helps your digestive system to kick in and work more efficiently? As you do the hard work of meditation for digestion more often, it will get easier and your bowels can begin to work better.