Do you just mix them with the grains or cook them first to get them gelatinized? What are the pros and cons of each method? What portion of the fermentables can be in flake form?
I use flaked maize (corn), flaked oats and flaked barley in a couple different recipes.
I just put them right in the main mash mixed in with all the grain. I have even put them through the mill a couple different occasions by accident without ill effect. I do tend to add 0.25-0.5lb rice hulls when using flaked oats to help with the sparge. But if your primary crush is good they grist should lauter fine anyway.
I always thought that the flaked grain process involved gelatinizing the starches already, so they don't need to be cooked or go through a cereal mash step. Someone will have to back that up or correct me (while I look it up myself and re-edit). This is not to say they shouldn't be mashed, because all these flaked adjuncts need to be mashed.
In general, my recipes have always used less than 10% of the total grist with these things. Flaked adjuncts tend to be used in smaller quantities than using whole corn or rice for example to lighten the body of a CAP or Light lager.
EDIT: So I looked and saw on a couple other forums and saw in John Palmer that most of these flaked grains are pre-gelatinized making them easier to work with from a cooking perspective. So they don't need further processing by the brewer prior to mashing. But they must be mashed.
Unless you are making a specific recipe that uses a lot of flaked grain such as a wheat beer, the flaked portion of a recipe is usually a very small percentage of the grain bill and should be considered more of a specialty grain contributing flavour, colour, mouthfeel rather than a significant amount of fermentable sugars. Assuming you are doing a full mash (not a grain tea) they just go right into the mash as you get them from the brew shop.
Don't crush them with your other grains.
Many people suggest layering the flaked grains over and inch or so of base malt to avoid a stuck mash from the gelatins forming a layer on your false bottom or screen but I find the act of doughing in mixes them all up anyway so I'm not sure if that's really very helpful. Often people will add some rice hulls with the flaked grains just to break it up a little more.