After choosing your eggs, it's time to start incubating.  The instructions that came with your machine will help you set the temperature to 99.5 degrees for a forced air model or 102 degrees for a still air model, at which point it's a good idea to let the incubator run empty for a day while you monitor the temperature and humidity and ensure it's working properly.  If there's any chance someone in your houshold will accidentally unplug the incubator in the next three weeks, tape the cord into the electric socket as insurance.  (Yes, I learned this the hard way.)

The main choice you have to make at the beginning of the incubation process is how to arrange the eggs --- vertically like they'd sit in an egg carton or horizontally the way they'd lie in a hen's nest.  Although the latter option sounds more natural, in practice I've had slightly better results with vertical incubation.  As the embryo grows, the highest point in the shell becomes an air pocket which the chick will poke its beak into shortly before hatching.  If this air pocket develops at the pointy end of the egg, the chick will find it difficult or impossible to hatch without help.  Setting the eggs vertically with the blunt end up helps ensure that the chick will be situated the right way inside the shell. 

If your incubator only allows you to lay your eggs horizontally, I wouldn't worry too much about it.  That said, some incubationists set their eggs inside an egg carton with the top cut off to allow them to incubate vertically even in a simple incubator.  More complicated incubators, like the Brinsea Octagon 20 I recommend, often have removable dividers that let you choose how to align your eggs.

No matter how you arrange them, you don't want your eggs shifting and hitting each other.  Egg turners that hold individual eggs make this point moot, but I find it helpful to add a piece of crumpled up paper in small gaps between less solidly touching eggs in our Brinsea Octagon 20 incubator.  This ensures that I have room to lay all of the eggs flat on the tray during the hatch, but that the eggs don't roll against each other and risk cracking as the turning cradle rotates the incubator.

The decisions you make during the early incubation period have a strong effect on how many healthy chicks eventually pop out of their shells.  Permaculture Chicken: Incubation Handbook covers deciding whether to candle, tips on turning the eggs, ways to keep the internal humidity at the proper level, and what to do if the power goes out.  Check out the 99 cent ebook and become a real incubation expert!

This post is part of our Chicken Incubation lunchtime series.  Read all of the entries: Permaculture Chicken: Incubation Handbook Why incubate? Choosing hatching eggs Filling in the incubator Chicks hatching