Every lane through it follows that centerline exactly.
Three sets of locks, five chambers: GatĂșn (3, lifting ships from the Atlantic to GatĂșn Lake), Pedro Miguel (1) and Miraflores (1, lowering them to the Pacific), all out in the middle of the isthmus, clear of Colon's and Balboa's marinas (which are drawn many times real size). Chambers are drawn about 1.5 nm apart, several times real size, so they're visible at full zoom (like the ships).
Each chamber has two lanes side by side, one per direction, and holds one ship per lane. A ship sails into a chamber and sits for 3 s while the water rises or falls, then sails on. If the next chamber is close (the rest of the same flight, or Pedro Miguel to Miraflores), it stays in its chamber until that one is free. Northbound and southbound ships never block each other.
A ship coming up to a busy chamber waits in line behind it, 1.6 nm behind the ship ahead, first come first served (recovery boats too). No cap on the line.
Engines are off in a chamber, in line and at the toll: no fuel burned, no wear. Nothing breaks down anywhere between the canal's entrance and exit. Fuel checks before departure only count sailing time, so they're unchanged.
Toll: a cargo ship entering the canal pays 20% of the leg's base pay (before any hub Pay bonus). It's logged, counted in Finances ("Canal tolls", per ship and overall), and taken off the profit reported when the ship leaves the port at the end of that leg. A ship without the money waits at the entrance ("Waiting for toll money", a red dot on the Ships tab) and goes once it can pay. Recovery boats (and ships they carry) pay nothing.
XP bonus: a delivery from a leg through the canal earns +50% XP for the company, the ship and the hub where it's unloaded, added to the other bonuses (a hub's +30% company XP becomes +80%).
On the map the canal is always drawn as a wide water channel across the isthmus (as are all the canals), wider as you zoom in. From 120 px per degree its chambers appear: two lanes each, with gates at the ends, the water darkening or lightening as a ship inside is lowered or lifted. Ships in the canal keep to the right-hand lane. "Panama Canal" is labeled at mid zoom, and each lock's name when zoomed in close.
Clicking a lock (once its chambers are drawn) opens a popup: for each direction, each chamber's ship ("Ever Bright, rising (2 s)", "coming in", "waiting to move on" or "empty") and who's waiting in line.
Ships already partway through it carry on without paying a toll.
A leg can pass several canals (Duluth to Rotterdam goes through the Soo Locks, the Welland Canal and the St. Lawrence Seaway). Each charges its own toll as the ship enters it, and each adds its XP bonus to the delivery.