One thing you might want to do when you're in Puerto Princesa (PP) is to take the Underground River and Honda Bay tours. At least that's what tourists who've been to PP would tell you. Well, I'd like to say the same primarily because I have immensely enjoyed both activities. I know you will too. If you are time-pressed and only have a day to spare in the city, then your best bet would be the Underground River tour, but make sure not to skip Honda Bay next time you're in PP. Rather, don't just spend a day in Puerto Princesa - there are several things to see and do that 2 days is not enough to enjoy what this city 'inside the forest' has to offer.
Island hopping in Honda Bay alone, for instance, will eat up half of your day so try to get up early and be at the wharf before 9am to beat hundreds of tourists that crank in. You know what they say about early birds getting the worm. Boat rental starts at 1,300 and they only have a handful, so when these boats are occupied, rental fees get a little higher. Don't asky why, I myself don't know the reason behind it.