Even The cheapest flight between Bangkok and Manila is very expensive it is hard to find flights under $300 . When doing research for my trip to the Philippines I was surprised at the cost to get there. I ended up flying from Bangkok to Singapore and then on to Manila via Clark in Angeles city which saved me over $100 dollars You can also go from Bangkok to Kuala Lumpur and then on to Angeles City which you can get a taxi or the local busses to Manila around 90 minutes away. by flying this way I pretty much wasted a day but the $100 dollars was worth it also I spent a night in Singapore in either direct which Singapore is one of my favorite cites for its melting pot atmosphere with all the great food and nightlife
The flights that I took was Air Asia from Bangkok to Singapore and then I took Tiger Air to Angeles City. I then took a bus that I caught just outside of the Angeles City airport which you have to take a taxi too and I might add that it is a rip off but there is nothing you can do about it as it is way to far to walk. Having a hotel pick you up is a good idea Margarita Station website where you can make reservations for Angeles City Hotels and arrange pick up from the Clark Airbase.
If you are looking for a cheap hotel in Manila Good luck I stayed at the Pension Natividad which was recommended to us it is a great budget hotel located downtown close to the Pan Pacific lots of good services nearby like internet and lots of good food. One note on the hotel if you are turned off by religion you might want to go somewhere else as they are heavy duty Catholics and there are Jesus and Saint pictures everywhere. They are also not friendly to having nocturnal guests as you would expect.