What the city is best for
Çanakkale should be planned by area, travel time and what you actually want to do. It works especially well for history, road trip, culture and nature. The main anchors are Troy, Gallipoli Peninsula, Çanakkale waterfront, Trojan Horse, Kilitbahir and Bozcaada day trip, but the value of the trip depends heavily on where you stay and how you structure the days.
The most useful bases are Çanakkale centre for ferry and evenings, Eceabat for Gallipoli access, Assos/Bozcaada side for wider coastal trip and near Troy only if focused on ruins. Choose short access to what you will do most, not just the lowest hotel price. For short stays, a better location often saves both time and transport.