Which goes to show that anywhere in the world there would be places that aren't safe at all. Holloway Road in London for instance is neither safe...in Lancaster Gate a lot of guests lost their bags although it's the Westminster Area and policemen are just lurking nearby.
I am pretty sure you will be safe in Manila as you will be with your friend who is a Filipino, he won't do stupid things to put you at risk. Manila was my second home and I would love to be back and enjoy it even for a couple of days.
I hope you will enjoy Manila and do keep safe!