Active Directory sites are comprised of IP subnets. In the AD Sites and Services console add all your IP subnets to the Subnets section. Then setup your various sites and assign IPs to the subnets.
If you have any specific sites which you want to replicate to each other you can override the default replications paths by editing site links. If you are doing this after setting up all your domain controllers you will need to go and move the domain controllers into the correct sites within the AD Sites and Services console.
DNS will take care of it self when you make the changes within the AD Sites and Services console.
Make sure that you setup at least one global catalog in each site, and make sure to pt the FSMO roles on DCs which make sense.