Build the file around the departure date and work backwards. Balance due, final documents, visa lead times and check-in windows all hang off it, and an agency that tracks them individually will always be reacting to whichever supplier shouts loudest.
Record who is on call and what they can see. The value of an agent is entirely in the moment something fails, and that moment does not respect office hours — a file that only opens on one person's laptop is a promise the agency cannot keep.
Reconcile commission properly. It arrives late, partially and from several suppliers at once, and without a line-by-line check it is genuinely common for a trip to be flown, enjoyed and never paid for.