Getting off a train at the right stop requires planning. It's a matter of physically pushing your way to a door before the train gets to the station. This presupposes you know where you will get off beforehand.
Newcomers to the system have no chance.
If you don't have a guide; forget it. Jeepneys and buses go everywhere but buses don't show route numbers. Instead, they show destinations.
Your best advice is to have a trusted guide who will not only save you money but can recommend sights along the way.
It is better usually to get a taxi but then you have the world wide taxi scam (the long way) to contend with. Some taxi companies are combating this at the airport by a pre-agreed fare system that works very well to ensure you pay the correct fare to your hotel and don't get ripped off.