Hi there, Mandy, and welcome to Scarleteen.
It sounds like your next step here needs to be having a few conversations with everyone involved, where you make sure that all three of you have the same understanding of what the parameters of all these relationships are. What I'd suggest is actually to have three different conversations: one with your friend, where you talk about the relationship you'd like to have with her and how you do or don't want to be involved with her boyfriend, one with the boyfriend, where you establish those wants and boundaries with him, and then a time for the three of you to sit down together and discuss all of this.
I can't give you a specific way to talk about the relationships the three of you have without it causing a problem, but not
talking about this is likely to cause more problems, if you all aren't on the same page about things (and it sounds like you aren't, right now).
In terms of safer sex, we definitely recommend condom use, but if he's using the same condom when having sex with both of you, that's not part of proper condom use; he should be swapping them out between partners. I don't know if you and your friend were practicing safer sex with use of barriers before her boyfriend entered the picture, but that's something you may want to talk about; in fact I suggest that safer sex practices and birth control be a part of the conversation the three of you have together. Our primer on safer sex is here, if you want a good reference point to start with: Safe, Sound & Sexy: A Safer Sex How-To