Will my son and i live in a different home when converting orthodox?

I am converting to Orthodox Judaism and have a son from a previous relationship (he is now 2 years old) My boyfriend/fiance is Jewish and we attend all the services and the standard procedures needed. My son's real father left while he was 8 months old and looks to my fiance as his ACTUAL father. My question is, will our son and i have to live apart from his adopted father when converting to orthodox? I have read that depending the Bet Din we can live in different quaters of the house, keeping the laws in order, etc.