Once the information is in hand, do not start entering services straight away. First make a tour project: the itinerary, how many nights in each location, how the traveller moves from one point to the next, and what kind of experiences to include.
Transfers: if a car transfer runs more than two hours, prefer a direct train.
The exception — the route stop: when a stop along the way can turn the transfer into an excursion, the car makes sense even beyond two hours. Example: Rome to Sorrento with a stop at Pompeii — a two-hour guided visit plus an hour for lunch. It is no longer a transfer but an experience.