Palawan, in general, is a haven of affordable inns and hotels, one of which is Casa Linda Inn.
It is conveniently located in the city, close to the port and airport, the Puerto Princesa cathedral, the market, and two of Pto. Princesa's famous restaurants. It is actually walking distance from Kinabuch's (where you can order tamilok, the mangrove worm delicacy) and Kahlui's but is tucked in a quiet street so you literally get transported to a quiet, garden and bamboo place.
You can contact them for room reservations and tour packages at casalind @ mozcom.com or call (048) 433 - 2606. They can also arrange massage services for you, just inquire at the desk. The staff is unbelievably friendly and accommodating and their tour affiliates are professionals.