On the last poly I took, I made the mistake of admitting that I was controlling my breathing. Now, I honestly thought the guy wanted "regular" breathing, for that is what he told me to do. The polygrapher may have been rusing me, or he may actually have had the machine on in accusing me- I don't know. (The reason I don't know is my probation officer asked me later if the guy ran the test on me, implying he may not have or in any case did not tell him the results).
IMHO, I would have to say that breathing CM's, unless you can really convolute them and do patterns within patterns, etc, are less desirable than mental CM's. I don't want to step on George's toes on this one, but it seems logical.
The polygrapher can always accuse you, whether he thinks you are using CM's or not. Also, if you totally control your breathing (which I did), I would have to give the interrogator the benefit that he can make out a single-layer pattern (like a consistent amplitude -and- frequency, which I did) or a diminishing amplitude pattern followed by apnea. Certainly, I think, he could make out a decreasing or increasing frequency pattern. Since breathing is controllable, and the ploy (oops, poly) guy knows this, I would suggest going with something mental or otherwise invisible (which I will do). I wouldn't take the risk of getting made.
Now, this is my sophomoric opinion and my own plan of action. I have read TLBTLD twice, the DODPI manual, and most of this site, and that's it. George and many of the more experienced posters here have more authority on this than do I, and if they disagree, I would defer to their views in a second...