House said my companions would be able to stay in the suit, but every time they leave they just go back to where I found them. How do I get them to stay? Also, it says I can only have one companion at a tim. When do I get the ability to have two?

I had the option to tell Boone to wait for me in the suite, and he did. E-DE on the other hand, seems to head back to the town where you acquire him.

As far as multiple companions goes, as far as I know you can only simultaneously have one humanoid companion, and one non-humanoid (ie, robot or animal) companion. So you can have Boone and E-DE at the same time, but you can never take another human along with Boone.