Once you are sure that your incubator is able to reach and maintain the correct heat and humidity, you are then ready to start collecting eggs.
The number of eggs that you collect will obviously depend on the size of your incubator.
Preparing Your Eggs
Do not collect and store the eggs for more than seven days. Wash the eggs in cold water, do not use detergent. Do not store eggs that are misshapen or cracked. Store the eggs pointed end down in egg trays in a cool room.
On the sixth day, switch on the incubator, having made sure that it is scrupulously clean.
On day seven, mark the eggs with a soft pencil (do not use a pen of any kind) and place in the incubator with the marks facing upwards. Ensure that the eggs do not touch each other and are not too near the incubator’s edges or the heat source.
The temperature will drop while you are doing this, but do not adjust, as it will soon rise to the correct temperature.
Daily Tasks
Keep daily records of the temperatures, humidity and turning of the eggs.
Eggs need to be turned at least three times a day, but preferably five or seven times. Some incubators have automatic turning mechanisms. If the eggs are simply being rocked, you should also physically turn them.
If yours is a still air incubator (no fans present), the temperature will vary quite dramatically over the length and breadth of the tray. Rotating the eggs and changing their position helps to overcome the effects of any temperature fluctuations. So the egg will spend time at the back, sides, and middle of the incubator over the period of incubation. To ensure each egg enjoys as equal a temperature as the others, change the position of the eggs relative to each other at each turn. The easiest way to do this is to move the front egg of the right hand side row to the rear left hand corner of the incubator, then make up the rest of what was the right hand side row by moving the rest of the row one egg to the front, on the left hand side. Then roll the remaining rows half a turn each to the right. It helps if the incubator is not chock-a-block full, for example if there is one empty row in the tray.
The machine should not be opened unnecessarily. In small machines, it is necessary to open for turning the eggs. Every time the lid or door is opened, most of the heat and humidity is lost, which results in fluctuating conditions for the next couple of hours until everything stabilises again. This is one of the main causes of poor hatch rates in small incubators. Having said that, eggs in their natural state would be cooled periodically each day as the broody hen moves about for food etc. In most small incubators this daily cooling is achieved when the incubator is opened for turning and no further cooling should be necessary.
Remember that you are imitating the behaviour of a brooding hen.
Candling
After ten days “candle” the eggs. This means that you use a light source to view how much space the embryo occupies within an egg. After about ten days, you should see the development of the embryo. If the egg appears to be black or solid, the chances are that a chick is developing inside. Discard the infertile eggs. Invest in, or make, an egg-candler ~ a tube fitted with a light bulb, a small egg size hole in the top, used to shine through the egg to check for fertility. Check eggs for fertility after seven days, then check again at 18 days before increasing the humidity and preparing for hatching. Always remove infertile/or dead eggs as soon as possible.
Stop turning the eggs two days prior to the estimated hatch date. For a list of length of incubation by species click here.
Hatching
You will start to see “pipping” when the little creature starts to peck at the shell from the inside. At hatching time, do not open the machine at all. A humidity drop at this time can result in chicks getting stuck in the shell. Rather, wait until most of the chicks have hatched, then open, move the chicks to a brooder and, if necessary, help any stuck chicks out of the shell.
Some breeders don’t help stuck chicks, in the belief that a stuck chick is usually a weakling that should die anyway. 
This is incorrect, for it is usually the mere fact of artificial incubation, and not the strength of the chick, that causes the problem in the first place.
But beware: a chick breaks through a shell in two distinct stages. In the first stage it punches through a single hole, and then takes a rest for a few hours. After its nap it starts pecking all the way around, and breaks out of the shell. Never attempt to assist a chick on the first stage because it will be a bloody mess that will die anyway. On the second stage, only break enough of the shell to release the chick, but do not remove it from the shell. There will be little or no blood at this stage. Once its head is free, it will be fine on its own if left in the incubator for a few hours to regain its strength.
Do not add feed while they are still in the incubator, as they will eat the insides of the shell and obtain nutrients from their feathers as they preen.
After 24-36 hours move them to a warm rearing house.
Remove the shells from the incubator and clean it thoroughly.