It refers to what sections in co-op city a route would be served first, over the other....
i.e.)
the old Qbx1 that went via "5-4-3-2-1" meant that, a bus heading towards co-op city would serve section 5 first, then onto section 4, section 3, section 2, then section 1...
the old Qbx1 via "1-2-3-4-5" means the opposite... a bus heading towards co-op city would first serve section 1, then section 2, then 3, then 4, then 5...