Hi Cameron 

It’s a natural part of the practice to spend so much time observing minute stuff that niggling questions (such as these) come up to bother us. But they should be taken as mere objects, noted, and dropped. Noting is what you do upon perceiving a moment of sense experience, no matter where or what it is. So if the abdomen is rising with an in-breath, note as rising. If something else is noticed, note that instead. If it seems nothing is happening, note the mental experience of thinking that nothing is happening. 

The Mahasi method is deceptively simple, and so the most common pitfall is adding complications into it, such as over-thinking, getting tied up in the content of thoughts instead of just noting them, etc. If you’ll take this from a stranger, the method is extremely powerful when done as instructed, but doing exactly as instructed seems to be the most difficult part for some yogis. Just relax into it, do it moment after moment, hour after hour, day after day, and insights cannot but unfold. There is nothing more to it. All the best!