Most people do clomid for days 5-9 of your cycle. I am not a dr and am not trying to be but I have heard that it regulates the time you 0 each month. So I wouldnt be afraid of it messing up your cycle. The ericsson method uses clomid (sperm spinning) to increase the chances of a girl. They don't give it to you if you are trying for a boy.
I am taking clomid for two reasons: I sufferd an ectopic in Jan and have one tube left and want to increase my chances to O from my good side. I am also taking it because I have heard that it can change your environment to favor girls. I'm just trying to do everything I can to give it my best go on 0+12. I will also be taking supplements, douch, hot baths, ect.