So many foods that we hear that are good for us yet, you also hear that they can also cause allergic reaction or have problems digesting. I LOVE tomatoes, but, I think I'm seeing bits and pieces in my BM's (Not sure)does that mean that the tomatoes aren't digesting all the way?

That's very normal. Especially the seeds and skin. I remember when I was in elementary school we went on a field trip to a sewage treatment plant. One thing that always stood out in my mind was the area where the treated sludge dries. It was loaded with tomato plants and they told us they came from everybody who ate tomatoes and had them pass thru their system .