If you are going to get around the island, you will need to run a bus in Palawan. The structure of doing so is pretty straight forward and they operate pretty regularly for the most part. The good news is they all pretty much work on the same terminal. This is not always the case in the Philippines.
As you would expect, there is buses that run north to El Nido and south to Brooke’s Point. There is other buses that make shorter run up and down the island. There is also oversized jeepney to that go to the villages off the main highway in both directions.
Bus in Palawan: the 411 on it all
If you go to San Juan in Puerto Princesa, to the north of the New Market you can see the bus terminal. There will be buses that are heading both directions lined up waiting for passengers. The southern trips are Bataraza, Rizal, Brooke’s Point, and Narra. The northern trips are Roxas, Port Barton, San Vicente, Taytay and of course, El Nido.
Different trips leave at different times and they all have different cost. None of them are over P400 though. Most are closer to half of that.
My suggestion would try and leave in the morning if you can. Traveling in Palawan takes lots of time. The island might not be wide but it is long as hell!
A word about Southern Palawan
As over 90% of tourism in the North, transportation in Southern Palawan is not that good. When you coming back to Puerto Princesa, you will need to plan accordingly. Depending where you are at, I would ask a local for the best time to get a bus. In some cases, there might only be one bus a day going to the capital city.
I would also try and plan to leave early as bus do break down in Palawan and you would like to have another bus coming by in 20-30 minutes if the one you are on does break down. Welcome to Palawan!