The prog supps will make it into your bloodstream. Supposedly they don't make it into the blood as much as the shots, but the prog makes it to your uterus (which is where it needs to be anyway). So, yes, your doc is measuring to see if you have a prog spike due to ovulating and due to the supplementation. The u/s will also show if there are empty follicles. That should give them a good idea of whether you ovulated.
And go ahead and insert the prog on that day unless they tell you not to. They're used to it
When's your beta? 4/8 or 4/9? Good luck!