In medicated cycles, I always had baseline scans on CD2 or 3 to check for cysts. If there was a functional cyst (meaning that it affects your estrogen levels) they wouldn't use fertility medication that cycle.
The scan wasn't any different b/c it was during AF. After all, you don't ever have to look at or touch the wand. I always felt a little bad for the tech, but it's part of the job and there's no avoiding it (and obviously they are not going to touch it after it's touched you, no matter what time of the month it is). Just remember to take out your tampon beforehand!
Then I would have my next scan at D12 usually, and maybe again the next day or the following day, depending on how the follies looked. If you sometimes ovulate earlier in the cycle, they might start monitoring a little earlier, like at D10.