“the stronghold of the house of El-berith.” Apparently, the temple of El-berith (“God of the Covenant”) had an especially fortified area known as the stronghold of the temple, and the people fled into it for safety. This tower may not have been in the city of Shechem, but close by Shechem.
“underground chamber.” This could have been an underground chamber under the tower. In 1 Sam. 13:6 the word refers to a cellar or cave.