Femara doesn't thin your lining out as much as clomid. They tend to recommend that more for us AMA ladies. But they both do about the same thing. I've not heard of it being taken WITH IVF meds, usually the stimming meds - gonal-f and menopur are what make the follicles grow. Though, I have heard of estrogen priming, so maybe that's how they're using it.
I did 4 cycles of femara with IUI and TI and I didn't have any major side effects except for headaches.