My father took his seat at the head of the table and began to pray.
Literal
Father [topic-は] table's head-seat's own seat [at-に] sat-down [and-て], prayer [object-を] began.
The お prefix on 祈り is honorific/beautifying. The te-form 着いて links two sequential actions: taking a seat, then beginning to pray. 上座 (かみざ, 'head seat') refers to the seat of honor at a dining table.