I leave all the chicks from one hatch together. (I get st. run when I can, because I am a softy and can't bear the thought of what hatcheries do with the extra males). Last time I ordered some chicks, I got 21 in the box, and 13 were males. When the boys start to crow and annoy the pullets, I start thinning them out. The smallest, early crow-ers might be culled as early as 10 weeks old. A lot depends on your plans for them. Some breeds, for example Leghorns, you might want to cull the males as soon as you can tell them apart since they are not very large as meat birds. You can go to the Meat Birds ETC section for more discussion of this aspect of chickens. Culling can be removing them from your flock by selling or giving them away, too.
You can start to tell as young as 3-4 weeks old that you have roosters, and how many. If you have a lot of them, that might be a good time to pen them separately, if you have the extra pen space.