You really want to have a family meeting where you all sit down together. Have a stick or something and only the person holding it can talk. Everyone gets a chance to express how they are feeling. Ground rules need to be laid.

Some suggestions:
Your daughter's room and the boy's room should be their own private spaces. They should be respected. If you daughter doesn't want to be around him she should be able to go into her room and he has to respect that and leave her alone while in there. And vice versa. Obviously communal areas are going to be open to all.

The other thing that I've heard time and again is that it causes a lot of problems and friction when you try to discipline someone else's child. Make sure that the rules are clearly laid out as are the consequences. You should leave discipline up to his dad whenever possible. If not possible you should try natural consequences such as "I'm sorry you chose to yell at me, that's not appropriate behavior. By yelling you've made the decision to spend some time in your room. I hope later you will choose to speak respectfully". This puts the behavior and decisions on him. You are not "punishing" him, he is making his own decisions and therefore choosing the consequence.

A lot of these things I've learned in parenting classes, from my T, and from professionals in the fields of health and child development. I hope some of them are useful to you.