The Administrator of USAID is a presidentially appointed and senate confirmed position. Under the Vacancies Reform Act the President can appoint another Senate confirmed official from anywhere else in the government to fill that spot for up to 210 days. Trump appointed Rubio to that role.

An acting administrator or agency head can then generally “detail” an employee from anywhere else in the government to serve as a deputy in a temporary basis, which Rubio did here. Agency heads generally have broad discretion to hire their deputies.