how to manually solder exposed-pad QFP package (Altera 144 pins)
Why do you heat it up from the bottom? You should use the hot air station from the top. Place the board over a solid surface and raised a bit on something. I use two metal L brackets from the hardware store. Then, using the hot air gun, slowly bring the board up to temperature. Ideally you should follow the profile of the solder paste (example below), but that's a bit hard to do with a hot air gun.

I like to take my time, and work around the edges of the chip package. You can start with your iron set at a fairly low air speed and temperature (240C), and get everything nice and toasty. After a few minutes increase the temperature of your iron (I got to about 350C) and get all the solder flowing.

You'll still likely burn the board some, but with this method it's minimized.