We use journals in every unit but only in one center at a time.
I have color-coded file folders, one color per grade. The student gets their folder and a journal page to write on at a particular center: this center may change from unit to unit but normally it is in the Bible Skills and Games center. The journal page has directed questions and the leader includes journaling time in his/her lesson time. The kids keep their papers in their journals and get them at Confirmation.
Some kids will eventually have 6 years worth of journaling papers if it works out right! They have been well received and these folders they get at confirmation are pretty special (this is our third year of rotation).