I visited Bohol as part of a trip in the Philippines in 2011, in part for research and photography for the Ecosystem Guides book "Rainforest of South-east Asia', and in part for photography & information for work as a lecturer & guide for upcoming expedition cruises in south-east Asia.
One of the reasons to go to Bohol was to check out a small 'backpackers lodge' called "Nuts Huts".
Even though there are plenty of place in the Philippines to stay near coral reefs and on islands and coasts (for example, Panagsama beach), there are not too many nature-based places to stay in the Philippines that are in or near the rainforest, in contrast to say Thailand, Mayalysia or even Indonesia.
The best place to stay at for nature buffs on Bohol is "Nuts Huts", because of their location. You are actually located in the jungle, on the banks of the Loboc river.
First, catch a ferry to the island of Bohol from Cebu city on Cebu to the port of Tagbilaran (or from the capital Manilla, although that is long way). From the port, get a taxi (up to 900 pesos if you are lazy..) or a combo of tricycle and jeepney (couple of hundred). Then, no matter what way you have arrived, you will have to get dropped off at the sign on the main road and no further! From here you have to walk past some rice paddy fields and huts down to a big flight of stairs. Please note, that it is a bit of a walk with a backpack! Walk down the stairs and you are finally at Nuts Huts!
Unfortunately, you will hear quite a bit of music through the forest from the tour boats on the river, from about 10am in the morning throughout the day. There are not many options for walking trails around the area. There is a trail along the opposite side of the river; this goes through some small villages and then past rice paddies and then into the town of Loboc. It gets confusing at times, just more or less keep near the river.
The restuarant looks out over the jungle and the rooms are along the river. I didn't spend much time in the huts. At dusk, you may spot some smaller flying fox about. In the morning there are (black-naped?) Orioles. The best place is the restauant, as it has a nice view of the jungle and you can usually see some birds, such as the Orioles, sunbirds and flowerpeckers.
Walking around the grounds there are also insects and reptiles to be spotted...
I have also spotlighted the endemic 'Philippines Scops Owl' along the stairs at night. There is a bird list at the counter put together by birders that have stayed there previously.
There are other things to do in the surrounding areas on the island of Bohol, including the Chocolate Hills and Tarsiers ...