After few hours of travelling, they reached Sicily, Amara was awake the whole time as she couldn't let her guard down so she guided Joshua after they reached the main city and directed him to a place where her apartment was located.
This apartment was bought by Michael for Amara during her training, she rarely visits this place and lives with Michael in his bungalow but this apartment was for her personal use.
She was free to use it as her office or could come here whenever she wants her own personal space.
Since, Dan, Vic, Jim and Carl worked with her on the mission they went to Vulcano island for, they were aware of this place as they met here once for one of the meetings. Without her explanation they understood why she must have brought them here.
She can't directly take Joshua to Michael's house. it is his secret location and people who they really trust are the only ones who are allowed there.