Put the boat up on some saw horses if you have them and pour water into the cockpit. Watch for drops of water to come out of the patch. Work these areas over again with the torch.
Now if you want to, you can use the torch on the inside of the boat to transition the plastic of the boat to the patch. This time you're smoothing the plastic of the boat onto the patch. I think this step isn't very necessary unless your patch is leaking.
Now all you need to do is sand the patch smooth. Unfortunately my boss never got around to bringing me a sander so our boats are a little rough.
After you sand the patch smooth, reattach all your components and you're ready to paddle!