This doesn’t seem to be a question as much as it is a statement. It sounds clear that you don’t like it and want it to stop — but seem to be wanting some guidance in how to deliver the message. Toward this end I am suggesting it is time for an important discussion in your relationship. There are five things that are going on that need some attention on your end before this can take place:
First, the boundaries are too muddied. Why does her friend move into your house—and then sleep at her place? Let’s get this cleared up because it makes no sense and certainly doesn’t sound like it was part of what you signed up for. What were you expecting, and is this still the case? This needs to be explained. Perhaps there is a good explanation that no one has explained (such as proximity to work) but this needs to be articulated so it can be understood.
Secondly, have you and she talked about this? It doesn’t seem so from your email. Does she know your discomfort? If she does is she ignoring it, defending against it, or dismissing it? Or, is it that you have simply not talked to her about it? She needs to understand your feelings. However, before you can express them to her you’ll need to understand them yourself. Take some time to sort this all through in your own mind. Do you feel betrayed? Are you angry? Disappointed? Miffed? Try to figure out what it is you are feeling so it can be accurately expressed.
Next, what prompted you to have him come stay with you? What were the arrangements and expectations? Somehow, if it were known that he’d move in and you’d be left alone in your place while he is with your girlfriend, you’d not have agreed to it. I think you need to chat with him about your initial thoughts with this arrangement. Does he know your feelings? Think a bit about what your point of view is and then have the discussion.
Is this a deal breaker? What if both of them (or either one of them) are not willing to change. What will you do? Do you end the relationship? Do you have him move out? Or do you find ways to cope? Think this through before saying something. While it is difficult to think about it is better to run through all the options in your mind first so you’ll have done some thinking about what you’ll do if things go south. None of these thoughts have to be acted on, but it is often a good idea to think about them so you can have a sense of where your thinking is at.
Finally, don’t sit on this too long. The resentment that will build from you not speaking up will eventually spill over and disrupt your relationship(s). Find a way to confront this situation sooner rather than later.