I've not taken the P2P bus in a long time but allocate at least 3-4 hours for the trip to account for traffic conditions. Either works in your case but I would probably do 8.5 hours. If your flight leaves from Terminal 3, you can just kill time at Newport City before checking in for your flight. (Back in the day when I took the bus, it took me about three hours with the bus stopping at SM City Clark before going to Manila.)

Check-in depends on your airline but the general rule seems to be 2-4 hours before. If you're flying PR or 5J, you may have more leeway with checking in earlier.