It's not easy to convey via written text so this short (very short!) [https://www.youtube.com/watch?v=i592NMuIKXg|video] probably does it best.
In essence, once you remove the IC, you want to clean it with your iron (~250C) to remove any underfill (if applicable) and also to remove any old lead-free solder. Some people like to wick away everything but wicking is inherently abrasive and if you can damage the IC if you're too agressive. Others like to use a concave tip and allow new leaded solder to naturally leave a light coating of solder on the pads. This same logic applies to the pads on the logic board BTW. In the linked video, you can see the IC has a light coat of solder on it.
Then you put the stencil over the IC and apply (leaded) solder paste. It's better when it's a bit dry, like in the video. Most solder paste is quite wet (the solders balls are in suspension in solder flux) so you have to let it dry a bit. Wet solder paste tends to expand and flow, therefore cross contaminating the holes in the stencil and you end up with an non-uniform distribution.
Then you heat the stencil, indirectly, with hot air until all the wells have molten. Remove the stencil and give another shot of hot air to reshape them properly and voila!
Now practice this 50 times and you might even be good at it ;>)! It is deceptively difficult and is an art form all it's own.