I'm currently working on a one-man show where the actor is the writer of the piece. He's been doing the show once every year or two over the last ten years. I worked on a one-woman show earlier this season where the actor was also the writer of the piece. It was a new production that had been work-shopped once.
On my current show, I've worked with the actor and the director several times before. When we get to a natural stopping point near a break, I call the break (after checking with the director) and they kind of take a break but often continue their dialogue as ideas come to them. My asm and I are free to take our breaks, but I usually hang out and listen. However, the director is really good about telling me anything that they come up with over the break. And he is really relaxed and our 10s are often 15s. For me, as long as the actor is happy, I just go with the flow.
On my show earlier this season, I didn't know the actor/playwright or the director. They were a bit more formal about the breaks, and I called them like I would in any show. The actor always had the freedom to tell me if she needed one earlier/longer than what was called. And as a side note, she had an uncanny sense of time and knew when an hour twenty had passed and we were due for a break without looking at a watch.
In both shows, I'm keeping careful track of the cuts/changes that are being made to the script so that the actor/writer and the theatre have an accurate version of the script used for the production. I also find that while the relationship with the actor/writer is very professional, it's a lot more personal than when working with a larger cast. In terms of show maintenance, on the show I did this spring she would riff and try new things, but she (and the director) had me keep an eye on pace. Just keep an open dialogue with the actor and the director.
Keep us posted; I hope all goes well with your show!