I was on Clomid for 3 cycles. I started testing on day 11 and for me the Clomid pushed back my Ovulation day to 16 or 17 (normally 14). I always went in for an ultrasound the day I got a positive LH test, sometimes again the next day. As for the BD, we did IUI usually the 2 days after I had the positive LH test, or whenever my follicles were big enough, which they tell from the ultrasound. The doctor would give me a shot to make me ovulate, before the IUI, or BD in your case. I also had a bloodtest run each month. My doctor tested different things each month, just to make sure. I think he tested Estradiol as well as progesterone to make sure it was high enough. I am not sure if this is the same with everyone, but sounds to me like your doctor is doing the same thing mine did.
I am now seeing a Reproductive Endocrinologist, as the Clomid did not work for me, but I know it has worked for many people and is a very inexpensive fix for some! We are trying Repronex (an injectible) this cycle and I will have to go in for 4 ultrasounds and 4 sets of bloodwork each cycle I am on this drug. I never thought having a baby would be so expensive....but well worth it in the end when you get to hold the precious gift. Good luck to you and your wife!
~ravae
PS - some of the side effects you can expect might be moodiness, hot flashes, night sweats and, for me, it made me very emotional. A small price to pay for a baby, if you ask me!!