The flaked version you chuck in with your mash. The flaked versions are more expensive though. For me
Corn: I only use polenta now. It is cheaper and I reckon it gives a smoother taste to the brew. It is also easy to use as corn starch gelatinization occurs at mash temps. You can pre cook it as per normal if you wish, but isn't required.
Wheat: To help avoid and haze in the beer, you can add a protein rest to your mash schedule. 50c for 10-15 minutes before raising to mash temp. It is only 10% in this recipe but I can almost guarantee without this step it will haze.
Rice: I use Jasmine rice and cook it as per normal before adding it to the mash. I put enough water in to cook the rice and absorb the remaining when the lid is left on. Make sure you break it up good in the mash though as it tends to clump. You can make it easier by scattering out the rice on a bench/baking paper and separate the grains with a fork. This will greatly help with mash efficiency.
If you ditch the rice you could leave it as is and the alcohol will be roughly 4.5% opposed to 4.9% or you could add another 500g of 2-row. It's up to you.