Somethings you sort of have to take it on faith. There is a bit of trial and error involved. But most people will start by following a recipe or a guide for what they want to cook. And that comes down to having some trust in whatever you’re using as a guide.
The term cooked, as most people use it refers to both the temperature of the item, its expected texture. The appearance of a cooked item is what differs most with using a precision cooker.
If you decide you want your 2" thick steak at 54C/130F because you like it medium-rare, you would set your Anova to this temperature, allow it to heat the water bath and drop your packaged steak in. Now, cooking is about heat penetration. It takes approximately 30 minutes for the heat to penetrate half an inch of meat (this varies with density, and a whole lot of other things, but is a good rule of thumb to use). For our example steak that is 2 inches thick it will take 2 hours for the core of the steak to reach the same temperature as the water bath. For something that is naturally tender, like a rib steak that may be all that is required. For a rump steak of the same thickness, you would probably want to give it some more time in the cooking bath to break down some of that harder working muscle fibre.
When people are saying that their food is not cooked after hours of time, they are most probably referring to the food not having the appearance they expect. This appearance is largely a product of the temperature at which it is cooked. Rare, medium rare, medium or well, is a product of the temperature and it is important to understand that.
I have seen people cooking pork at 57C/135F (which is a perfectly fine temperature for pork) for the required amount of time and complain that the meat is still raw because it’s pink. Of course, it’s not raw at all. It is perfectly cooked to the rare side of medium. They were expecting to see white pork, but they have not understood what to expect from the temperature that they have used. If you wish to get white pork you need to use a higher temperature. Around 60C/140F will give a finish to pork with only the slightest hint of pink particularly around any bones. 63C/145F will give you solid white. Many people still have an aversion to eating medium rare pork, although it is safe to do so. Individuals that exclaim loudly about having followed directions but their pork is still raw probably fall into this category.
It is important to understand what varying the temperature will do to the appearance of what you’re cooking. Chicken cooked sous vide may also display some pink hues. Once again, provided it has been cooked to pasteurisation (a product of time at temperature) it is perfectly safe to eat.
Hopefully this has helped your understanding a little.