Hi Roy,
Philippines is generally safe to travel, but pay attentions to your belongings on long bus rides. Pick pockets are always looking for easy targets, but if you follow basic precautions you'll do just fine.
For 2 weeks I suggest you to visit Manila for a day or two, take a 5 days trip to North Luzon including Baguio city, Banaue-rice terraces and Sagada , where the famous hanging coffins are then head down to one of the islands.
My favorite is Palawan, you can easily spend a week here traveling from North to South. Or you might choose to catch a flight to Borocay for a few days, then a connection to Tagbilaran City - Bohol and explore the Chocolate Hills, meet the tarsier (smallest monkey type of creature), see the flock of dolphins swimming by your boat and hop to the surrounding islands. Snorkeling and diving are gr8 around Bohol. Don't stay in the city, choose one of the beach resorts.
Have an awesome time in the Philippines!