What is the best way for me to discuss this issue with my roommate?

We’ve had a healthy relationship (both girls) and we live in an apartment off campus. We respect each other’s time and space and almost never have issues. The past two months I’ve been staying at a friends place to avoid triggering my hives (she knew this.) Once the temp cooled down I started spending more time at the apartment. We’re close friends but because of this we haven’t been hanging out as often as usual. I got a text saying her friend/my acquaintance asked if he could stay in our living room for the rest of the semester because of problems at home and would split rent with us. She asked if I cared and that if I did, she could tell him no. I felt bad and explained why I had to say no. My parents are paying for my rent and they’d be upset knowing a boy was sleeping here that long. I don’t feel comfortable with hiding things from my parents. They also like to randomly drop by and sometimes I have to babysit my sister. She however, is on financial aid and usually gets notice of if her family is visitng. She said she understood.

The boy has been sleeping here the past couple of days and I don’t know how long he plans on staying, they didn’t run this through me either.
I have no clue what’s going on, but it’s awkward because I can’t go in the kitchen without feeling uncomfortable because he’s usually asleep. I can’t watch tv because he’s usually here when I have free time. I feel bad that I might wake him when I come home from my morning classes and late night studying. This whole situation makes me feel uncomfortable because I feel like he’s in my personal space. I also feel like a boundary has been crossed since I expressed how I felt about him staying here long term and nothing has been run through me about his staying now.

I really like the relationship that I have with my roommate, but how can I discuss this with her without looking insensitive?