Usually they start the 'defrosting' process sometime (I think is about 36-48 hours) before the FET time. My understanding is they know pretty quickly whether that has been successful or not, and if not they will attempt another and so on, until they get one which they consider 'viable'.

I have always had bad side effects from Clomid too - Im not exactly sure why you would have to take it during a FET, but best to call them up and check that out - Im sure they wont mind you calling and too bad if they do! You are the 'customer' so dont worry about it.

Hope that has helped a little bit..