After putting his body in the pit they covered it with a pile of stones. This can be stated more clearly. Alternate translation: "they covered his body with a huge pile of stones" (See: [[rc://en/ta/man/translate/figs-explicit]])
Here "all Israel" refers to the Israelite soldiers. The word "fled" means "ran away." Alternate translation: "while all the Israelite soldiers ran away" (See: [[rc://en/ta/man/translate/figs-synecdoche]])