Riding a jeepney is easy. The route is painted on the side of the jeep, but often that's not visible when the jeep is coming at you head on. Moreover, the destination is sometimes painted in a weird font and hard to read. The best place to look is the little tag mounted on to the top of every jeep, bearing the route number. If you're not familiar with the routes yet, check the destination by reading the little plastic sign dangling inside the front window.
You flag a jeep down just like you would a taxi. Just stick your finger in the air when you see one. It'll immediately pull up so just scramble on. Be careful not to hit your head; jeep ceilings are low and you'll have to walk in a crouched position.
Now, technically, you are not supposed to get on just anywhere. There are PUJ stops at predetermined locations. Jeeps which allow passengers to board in a "No Stopping" zone get busted by the traffic wardens - which are plentiful in Cebu City. In fact, talking to jeep drivers, there number one complaint is not the traffic wardens, nor the traffic, but the passengers, who have a propensity to board and disembark just about anywhere.
But don't worry about that; the customer is king, and if the jeep driver gets busted by CITOM - the traffic regulatory agency of Cebu City - for letting you board in a "No Stopping" zone, it's not your problem. Jeeps are eager to gather as many passengers as possible, and unless traffic conditions are really bad and a traffic warden is in plain view, the jeep will screech to a halt no matter where you are, even in a "No Stopping" zone. Having said that, if it's your first time to ride a jeep, you'd better stick to the PUJ stops until you get a feel of how things work.
The easiest place to board a jeep is at a terminal. The terminals act as nodes connecting different routes. There are several terminals in Cebu: at Ayala; at SM; next to the LTO on Bacalso; opposite White Gold restaurant. The thing about terminals is that the jeeps usually wait until they are full before departing.
You can pay anytime you like: when you get on, halfway through your journey, or when you get off. I don't know how they do it, but drivers and conductors manage to keep track of all passengers. If a jeep has a conductor, you can pay either the conductor or the driver. In developed countries there are usually rules about disturbing the driver while a bus is in transit; those rules do not apply here. You can talk to the driver or hand him money whenever you wish.
If you pay in advance or before the jeep reaches your destination, the conductor or driver may ask you where you are going, or hold up the index finger - asking whether you will be paying for just one length. Currently jeep fares are PhP 5.50 for the first five kilometers and PhP 1.00 for every succeeding kilometer. In practice, most jeeps do not collect the 50 centavos and round the amount down to the nearest peso.
You may be puzzled why, when a jeep is empty, passengers will prefer to sit at the back of jeep, rather than in the front. This is because the payment of fares relies on a uniquely Filipino system. Fares are handed from passenger to passenger until they reach the driver (or conductor). Your 20 peso note may pass through the hands of as many as seven passengers before reaching the driver; your change will travel a similar route making its way back to you. Consequently, the passengers seated in the front and in the middle find themselves constantly handling other people's money.
Getting off a jeep is a bit harder than getting on. Clang a coin against the metal railing, or slap your hand against the side of the jeep, while yelling lugar lang. This signals the driver that you wish to get off.
Jeeps run at all times of the day and night. The number of jeeps on the road is determined by customer demand; needless to say, you'll have fewer jeeps at 2 AM than at 6 PM. The system works exceedingly well - I'd venture a wager that Cebuanos spend far less time waiting for public transportation than residents in European cities - and seems to be proof that the less governments interfere with the transportation market, the better.