The Hotel Sogo Network has a lot of options in Manila and other cities.
The cheapest that I found on the Internet was the Sogo at train station called "Monumento". During the week the prices are: 6h/495P; 12h/630P; 24h/995P. On weekends they are: 6hs / 630P; 10h / 815P; 12h / 910P; 24h / 1100P.
To reach the "Monumento" Station, from the Ninoy Aquino International Airport (Terminal 3), you can take a bus (White Bus. Go out of the Airport Exit, turn right and go until the end). It cost 20P and takes you even to EDSA Train Station (in that station has a branch Sogo, but it's more expensive). The bus runs each 20 minutes. more or less. And It takes about 20 minutes until the EDSA Station.
To catch the train to "Monumento" station you must take the LRT line. The ticket costs 30P until "Monumento" station (here you pay different values depending on the final destination). The trip takes about 40 minutes (16 stations).
The Hotel is almost inside the station. You don't need go out on the street.
The Hotel hasn't check-in time not even check-out time. You have X hours after check-in (anytime).
They serve several types of food, at the room, with fair prices.
The Hotel seems a Motel, but is very clean and it's good option for maximum 24h and budget travellers.
There is a 7&11 in the other side of the street. At night, outside, seems not a safe place.
There are a small shopping (Victoria Shopping Mall) close to 7&11, with food court, McDonalds, a Daiso, local to take Passport photo (6 photos / 60P), a Do It Yourself store, a supermarket and several others stores.
Reserve about 1: 30h to return to the airport.