When the u. s. form the government of puerto rico, who chose the governor and upper house of the legislature of the new u. s. territory?

President McKinley appointed Charles Herbert Allen as Governor of Puerto Rico from 1900-1901. He did not become effective in his political endeavors in Puerto Rico. His term experienced criticism by different historians. The economic problems manifested on high tariffs and mostly taxes. His term made a low annual budget in 1897.  The land was not productively used which could have been a help for the people. 
Due to this reduced overhead, the island should have had a substantial budget surplus, but Allen's administration did not provide many benefits for the people. He made some wrong decisions on building roads and infrastructures and have insufficient schools for people.