I think you'll be fine using the ID.
I built my first offset this past spring (20"x46"x3/8" CC & 20"x24"x3/8 FB. I went with an oversized FB) using pipe. when I put it into the calculator, I used OD measurements. I'm very happy with how it came out, and how it cooks.
Currently, me and my daughter are building a RF for her. And with her smoker, I'm using the ID measurements to see if it makes a differance. The only thing that I noticed, according to the calculator, is that the throat is a little larger using the ID measurements.
I'm also very new at this, so I would wait to hear from one of the more experienced guys or gals that can help you better.
Good luck, and post pics of your build as you go.