@Dregenburn Based on what we know so far, it appears so that they don't really live together per-se.
Whenever Souta enters Nei-san's apartment, he says "ojamashimasu" (sorry for the intrusion), instead of "tadaima" (I'm home), so I'm assuming it's not his home.
but I'm pretty sure they're going out, and looks like Souta-kun spends the time after school, at Nei-san's place, probably every day.
Also, yeah. "turtle." Soooo cuuute!!